Source Name	Provider	Material Type	Term Source REF	Characteristics[Organism]	Term Source REF	Characteristics[Sex]	Term Source REF	Characteristics[DiseaseState]	Term Source REF	Comment[OCG Cohort]	Sample Name	Material Type	Term Source REF	Characteristics[OrganismPart]	Term Source REF	Description	Protocol REF	Performer	Extract Name	Material Type	Term Source REF	Comment[SRA_SAMPLE]	Protocol REF	Performer	Extract Name	Comment[LIBRARY_LAYOUT]	Comment[LIBRARY_SOURCE]	Comment[LIBRARY_STRATEGY]	Comment[LIBRARY_SELECTION]	Comment[NOMINAL_LENGTH]	Comment[LIBRARY_NAME]	Comment[SRA_EXPERIMENT]	Description	Protocol REF	Performer	Date	Assay Name	Technology Type	Term Source REF	Comment[SPOT_LENGTH]	Protocol REF	Parameter Value[Software Versions]	Protocol REF	Derived Array Data File	Comment[SRA_RUN]	Comment[SRA_FILE_URI]	Comment[OCG Data Level]	Comment[ASSEMBLY_NAME]	Protocol REF	Protocol REF	Derived Array Data File	Comment[OCG Data Level]	Protocol REF	Derived Array Data File	Comment[OCG Data Level]	Protocol REF	Derived Array Data File	Comment[OCG Data Level]
TARGET-10-SJMPAL017974	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood B Acute Lymphoblastic Leukemia	NCIt	Discovery	TARGET-10-SJMPAL017974-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-10-SJMPAL017974-09A.1-01D	DNA	EFO	SRS1761111	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-10-SJMPAL017974-09A.1-01D A59150 library	PAIRED	GENOMIC	WGS	RANDOM	473	A59150	SRX2238819	"WGS analysis of mixed phenotype acute leukemia sample TARGET-10-SJMPAL017974-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-10-SJMPAL017974-09A.1-01D A59150 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59150_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634851	@dbgap@:reads/SRP011999/SRS1761111/SRX2238819/SRR5634851/SRR5634851.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-10-SJMPAL017974.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-10-SJMPAL017974	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood B Acute Lymphoblastic Leukemia	NCIt	Discovery	TARGET-10-SJMPAL017974-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-10-SJMPAL017974-09A.1-01D	DNA	EFO	SRS1761111	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-10-SJMPAL017974-09A.1-01D A59150 library	PAIRED	GENOMIC	WGS	RANDOM	473	A59150	SRX2238819	"WGS analysis of mixed phenotype acute leukemia sample TARGET-10-SJMPAL017974-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-10-SJMPAL017974-09A.1-01D A59150 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59150_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634851	@dbgap@:reads/SRP011999/SRS1761111/SRX2238819/SRR5634851/SRR5634851.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-10-SJMPAL017974-09A.1-01D.fusion.vcf	3						
TARGET-10-SJMPAL017974	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood B Acute Lymphoblastic Leukemia	NCIt	Discovery	TARGET-10-SJMPAL017974-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-10-SJMPAL017974-09A.1-01D	DNA	EFO	SRS1761111	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-10-SJMPAL017974-09A.1-01D A59150 library	PAIRED	GENOMIC	WGS	RANDOM	473	A59150	SRX2238819	"WGS analysis of mixed phenotype acute leukemia sample TARGET-10-SJMPAL017974-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-10-SJMPAL017974-09A.1-01D A59150 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59150_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634851	@dbgap@:reads/SRP011999/SRS1761111/SRX2238819/SRR5634851/SRR5634851.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-10-SJMPAL017974-09A.1-01D.indel.vcf	3						
TARGET-10-SJMPAL017974	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood B Acute Lymphoblastic Leukemia	NCIt	Discovery	TARGET-10-SJMPAL017974-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-10-SJMPAL017974-09A.1-01D	DNA	EFO	SRS1761111	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-10-SJMPAL017974-09A.1-01D A59150 library	PAIRED	GENOMIC	WGS	RANDOM	473	A59150	SRX2238819	"WGS analysis of mixed phenotype acute leukemia sample TARGET-10-SJMPAL017974-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-10-SJMPAL017974-09A.1-01D A59150 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59150_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634851	@dbgap@:reads/SRP011999/SRS1761111/SRX2238819/SRR5634851/SRR5634851.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-10-SJMPAL017974.quality_tagged.vcf	3						
TARGET-10-SJMPAL017974	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood B Acute Lymphoblastic Leukemia	NCIt	Discovery	TARGET-10-SJMPAL017974-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-10-SJMPAL017974-09A.1-01D	DNA	EFO	SRS1761111	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-10-SJMPAL017974-09A.1-01D A59150 library	PAIRED	GENOMIC	WGS	RANDOM	473	A59150	SRX2238819	"WGS analysis of mixed phenotype acute leukemia sample TARGET-10-SJMPAL017974-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-10-SJMPAL017974-09A.1-01D A59150 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59150_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634851	@dbgap@:reads/SRP011999/SRS1761111/SRX2238819/SRR5634851/SRR5634851.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-10-SJMPAL017974-09A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-10-SJMPAL017974-09A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-10-SJMPAL017974	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood B Acute Lymphoblastic Leukemia	NCIt	Discovery	TARGET-10-SJMPAL017974-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-10-SJMPAL017974-09A.1-01D	DNA	EFO	SRS1761111	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-10-SJMPAL017974-09A.1-01D A59150 library	PAIRED	GENOMIC	WGS	RANDOM	473	A59150	SRX2238819	"WGS analysis of mixed phenotype acute leukemia sample TARGET-10-SJMPAL017974-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-10-SJMPAL017974-09A.1-01D A59150 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59150_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634851	@dbgap@:reads/SRP011999/SRS1761111/SRX2238819/SRR5634851/SRR5634851.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-10-SJMPAL017974.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-10-SJMPAL017974	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood B Acute Lymphoblastic Leukemia	NCIt	Discovery	TARGET-10-SJMPAL017974-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-10-SJMPAL017974-09A.1-01D	DNA	EFO	SRS1761111	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-10-SJMPAL017974-09A.1-01D A59150 library	PAIRED	GENOMIC	WGS	RANDOM	473	A59150	SRX2238819	"WGS analysis of mixed phenotype acute leukemia sample TARGET-10-SJMPAL017974-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-10-SJMPAL017974-09A.1-01D A59150 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59150_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634851	@dbgap@:reads/SRP011999/SRS1761111/SRX2238819/SRR5634851/SRR5634851.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-10-SJMPAL017974-09A.1-01D_TARGET-10-SJMPAL017974-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-10-SJMPAL017974-09A.1-01D_TARGET-10-SJMPAL017974-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-10-SJMPAL017974	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood B Acute Lymphoblastic Leukemia	NCIt	Discovery	TARGET-10-SJMPAL017974-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-10-SJMPAL017974-09A.1-01D	DNA	EFO	SRS1761111	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-10-SJMPAL017974-09A.1-01D A59150 library	PAIRED	GENOMIC	WGS	RANDOM	473	A59150	SRX2238819	"WGS analysis of mixed phenotype acute leukemia sample TARGET-10-SJMPAL017974-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-10-SJMPAL017974-09A.1-01D A59150 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59150_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634851	@dbgap@:reads/SRP011999/SRS1761111/SRX2238819/SRR5634851/SRR5634851.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-10-SJMPAL017974-09A.1-01D_TARGET-10-SJMPAL017974-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-10-SJMPAL017974-09A.1-01D_TARGET-10-SJMPAL017974-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-10-SJMPAL017974.combined_somatic_snvs.tab_delimited.txt	3
TARGET-10-SJMPAL017974	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood B Acute Lymphoblastic Leukemia	NCIt	Discovery	TARGET-10-SJMPAL017974-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-10-SJMPAL017974-14A.1-01D	DNA	EFO	SRS1761162	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-10-SJMPAL017974-14A.1-01D A59259 library	PAIRED	GENOMIC	WGS	RANDOM	436	A59259	SRX2238870	"WGS analysis of normal sample TARGET-10-SJMPAL017974-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-10-SJMPAL017974-14A.1-01D A59259 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59259_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634838	@dbgap@:reads/SRP011999/SRS1761162/SRX2238870/SRR5634838/SRR5634838.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-10-SJMPAL017974.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-10-SJMPAL017974	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood B Acute Lymphoblastic Leukemia	NCIt	Discovery	TARGET-10-SJMPAL017974-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-10-SJMPAL017974-14A.1-01D	DNA	EFO	SRS1761162	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-10-SJMPAL017974-14A.1-01D A59259 library	PAIRED	GENOMIC	WGS	RANDOM	436	A59259	SRX2238870	"WGS analysis of normal sample TARGET-10-SJMPAL017974-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-10-SJMPAL017974-14A.1-01D A59259 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59259_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634838	@dbgap@:reads/SRP011999/SRS1761162/SRX2238870/SRR5634838/SRR5634838.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-10-SJMPAL017974.quality_tagged.vcf	3						
TARGET-10-SJMPAL017974	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood B Acute Lymphoblastic Leukemia	NCIt	Discovery	TARGET-10-SJMPAL017974-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-10-SJMPAL017974-14A.1-01D	DNA	EFO	SRS1761162	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-10-SJMPAL017974-14A.1-01D A59259 library	PAIRED	GENOMIC	WGS	RANDOM	436	A59259	SRX2238870	"WGS analysis of normal sample TARGET-10-SJMPAL017974-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-10-SJMPAL017974-14A.1-01D A59259 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59259_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634838	@dbgap@:reads/SRP011999/SRS1761162/SRX2238870/SRR5634838/SRR5634838.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-10-SJMPAL017974-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-10-SJMPAL017974-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-10-SJMPAL017974	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood B Acute Lymphoblastic Leukemia	NCIt	Discovery	TARGET-10-SJMPAL017974-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-10-SJMPAL017974-14A.1-01D	DNA	EFO	SRS1761162	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-10-SJMPAL017974-14A.1-01D A59259 library	PAIRED	GENOMIC	WGS	RANDOM	436	A59259	SRX2238870	"WGS analysis of normal sample TARGET-10-SJMPAL017974-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-10-SJMPAL017974-14A.1-01D A59259 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59259_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634838	@dbgap@:reads/SRP011999/SRS1761162/SRX2238870/SRR5634838/SRR5634838.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-10-SJMPAL017974.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-10-SJMPAL017974	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood B Acute Lymphoblastic Leukemia	NCIt	Discovery	TARGET-10-SJMPAL017974-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-10-SJMPAL017974-14A.1-01D	DNA	EFO	SRS1761162	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-10-SJMPAL017974-14A.1-01D A59259 library	PAIRED	GENOMIC	WGS	RANDOM	436	A59259	SRX2238870	"WGS analysis of normal sample TARGET-10-SJMPAL017974-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-10-SJMPAL017974-14A.1-01D A59259 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59259_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634838	@dbgap@:reads/SRP011999/SRS1761162/SRX2238870/SRR5634838/SRR5634838.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-10-SJMPAL017974-09A.1-01D_TARGET-10-SJMPAL017974-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-10-SJMPAL017974-09A.1-01D_TARGET-10-SJMPAL017974-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-10-SJMPAL017974	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood B Acute Lymphoblastic Leukemia	NCIt	Discovery	TARGET-10-SJMPAL017974-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-10-SJMPAL017974-14A.1-01D	DNA	EFO	SRS1761162	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-10-SJMPAL017974-14A.1-01D A59259 library	PAIRED	GENOMIC	WGS	RANDOM	436	A59259	SRX2238870	"WGS analysis of normal sample TARGET-10-SJMPAL017974-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-10-SJMPAL017974-14A.1-01D A59259 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59259_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634838	@dbgap@:reads/SRP011999/SRS1761162/SRX2238870/SRR5634838/SRR5634838.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-10-SJMPAL017974-09A.1-01D_TARGET-10-SJMPAL017974-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-10-SJMPAL017974-09A.1-01D_TARGET-10-SJMPAL017974-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-10-SJMPAL017974.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-PAREAT	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAREAT-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAREAT-09A-01D	DNA	EFO	SRS1761188	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAREAT-09A-01D A59128 library	PAIRED	GENOMIC	WGS	RANDOM	464	A59128	SRX2238897	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAREAT-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-PAREAT-09A-01D A59128 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59128_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634849	@dbgap@:reads/SRP011999/SRS1761188/SRX2238897/SRR5634849/SRR5634849.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-PAREAT.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PAREAT	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAREAT-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAREAT-09A-01D	DNA	EFO	SRS1761188	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAREAT-09A-01D A59128 library	PAIRED	GENOMIC	WGS	RANDOM	464	A59128	SRX2238897	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAREAT-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-PAREAT-09A-01D A59128 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59128_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634849	@dbgap@:reads/SRP011999/SRS1761188/SRX2238897/SRR5634849/SRR5634849.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-PAREAT-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-PAREAT.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-PAREAT	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAREAT-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAREAT-09A-01D	DNA	EFO	SRS1761188	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAREAT-09A-01D A59128 library	PAIRED	GENOMIC	WGS	RANDOM	464	A59128	SRX2238897	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAREAT-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-PAREAT-09A-01D A59128 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59128_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634849	@dbgap@:reads/SRP011999/SRS1761188/SRX2238897/SRR5634849/SRR5634849.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-PAREAT-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-PAREAT.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-PAREAT	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAREAT-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAREAT-09A-01D	DNA	EFO	SRS1761188	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAREAT-09A-01D A59128 library	PAIRED	GENOMIC	WGS	RANDOM	464	A59128	SRX2238897	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAREAT-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-PAREAT-09A-01D A59128 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59128_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634849	@dbgap@:reads/SRP011999/SRS1761188/SRX2238897/SRR5634849/SRR5634849.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-PAREAT-09A-01D.indel.vcf	3						
TARGET-15-PAREAT	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAREAT-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAREAT-09A-01D	DNA	EFO	SRS1761188	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAREAT-09A-01D A59128 library	PAIRED	GENOMIC	WGS	RANDOM	464	A59128	SRX2238897	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAREAT-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-PAREAT-09A-01D A59128 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59128_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634849	@dbgap@:reads/SRP011999/SRS1761188/SRX2238897/SRR5634849/SRR5634849.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-PAREAT.quality_tagged.vcf	3						
TARGET-15-PAREAT	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAREAT-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAREAT-09A-01D	DNA	EFO	SRS1761188	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAREAT-09A-01D A59128 library	PAIRED	GENOMIC	WGS	RANDOM	464	A59128	SRX2238897	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAREAT-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-PAREAT-09A-01D A59128 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59128_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634849	@dbgap@:reads/SRP011999/SRS1761188/SRX2238897/SRR5634849/SRR5634849.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-PAREAT-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-PAREAT-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-PAREAT	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAREAT-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAREAT-09A-01D	DNA	EFO	SRS1761188	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAREAT-09A-01D A59128 library	PAIRED	GENOMIC	WGS	RANDOM	464	A59128	SRX2238897	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAREAT-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-PAREAT-09A-01D A59128 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59128_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634849	@dbgap@:reads/SRP011999/SRS1761188/SRX2238897/SRR5634849/SRR5634849.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PAREAT.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PAREAT	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAREAT-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAREAT-09A-01D	DNA	EFO	SRS1761188	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAREAT-09A-01D A59128 library	PAIRED	GENOMIC	WGS	RANDOM	464	A59128	SRX2238897	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAREAT-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-PAREAT-09A-01D A59128 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59128_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634849	@dbgap@:reads/SRP011999/SRS1761188/SRX2238897/SRR5634849/SRR5634849.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PAREAT-09A-01D_TARGET-15-PAREAT-15A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-PAREAT-09A-01D_TARGET-15-PAREAT-15A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-PAREAT	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAREAT-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAREAT-09A-01D	DNA	EFO	SRS1761188	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAREAT-09A-01D A59128 library	PAIRED	GENOMIC	WGS	RANDOM	464	A59128	SRX2238897	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAREAT-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-PAREAT-09A-01D A59128 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59128_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634849	@dbgap@:reads/SRP011999/SRS1761188/SRX2238897/SRR5634849/SRR5634849.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PAREAT-09A-01D_TARGET-15-PAREAT-15A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-PAREAT-09A-01D_TARGET-15-PAREAT-15A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PAREAT.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-PAREAT	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAREAT-15A	organism part	EFO	Bone Marrow	NCIt	"Fibroblasts from Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAREAT-15A-01D	DNA	EFO	SRS1761176	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAREAT-15A-01D A59238 library	PAIRED	GENOMIC	WGS	RANDOM	447	A59238	SRX2238884	"WGS analysis of normal sample TARGET-15-PAREAT-15A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-PAREAT-15A-01D A59238 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59238_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634846	@dbgap@:reads/SRP011999/SRS1761176/SRX2238884/SRR5634846/SRR5634846.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-PAREAT.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PAREAT	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAREAT-15A	organism part	EFO	Bone Marrow	NCIt	"Fibroblasts from Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAREAT-15A-01D	DNA	EFO	SRS1761176	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAREAT-15A-01D A59238 library	PAIRED	GENOMIC	WGS	RANDOM	447	A59238	SRX2238884	"WGS analysis of normal sample TARGET-15-PAREAT-15A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-PAREAT-15A-01D A59238 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59238_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634846	@dbgap@:reads/SRP011999/SRS1761176/SRX2238884/SRR5634846/SRR5634846.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-PAREAT.quality_tagged.vcf	3						
TARGET-15-PAREAT	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAREAT-15A	organism part	EFO	Bone Marrow	NCIt	"Fibroblasts from Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAREAT-15A-01D	DNA	EFO	SRS1761176	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAREAT-15A-01D A59238 library	PAIRED	GENOMIC	WGS	RANDOM	447	A59238	SRX2238884	"WGS analysis of normal sample TARGET-15-PAREAT-15A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-PAREAT-15A-01D A59238 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59238_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634846	@dbgap@:reads/SRP011999/SRS1761176/SRX2238884/SRR5634846/SRR5634846.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-PAREAT-15A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-PAREAT-15A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-PAREAT	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAREAT-15A	organism part	EFO	Bone Marrow	NCIt	"Fibroblasts from Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAREAT-15A-01D	DNA	EFO	SRS1761176	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAREAT-15A-01D A59238 library	PAIRED	GENOMIC	WGS	RANDOM	447	A59238	SRX2238884	"WGS analysis of normal sample TARGET-15-PAREAT-15A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-PAREAT-15A-01D A59238 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59238_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634846	@dbgap@:reads/SRP011999/SRS1761176/SRX2238884/SRR5634846/SRR5634846.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PAREAT.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PAREAT	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAREAT-15A	organism part	EFO	Bone Marrow	NCIt	"Fibroblasts from Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAREAT-15A-01D	DNA	EFO	SRS1761176	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAREAT-15A-01D A59238 library	PAIRED	GENOMIC	WGS	RANDOM	447	A59238	SRX2238884	"WGS analysis of normal sample TARGET-15-PAREAT-15A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-PAREAT-15A-01D A59238 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59238_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634846	@dbgap@:reads/SRP011999/SRS1761176/SRX2238884/SRR5634846/SRR5634846.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PAREAT-09A-01D_TARGET-15-PAREAT-15A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-PAREAT-09A-01D_TARGET-15-PAREAT-15A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-PAREAT	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAREAT-15A	organism part	EFO	Bone Marrow	NCIt	"Fibroblasts from Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAREAT-15A-01D	DNA	EFO	SRS1761176	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAREAT-15A-01D A59238 library	PAIRED	GENOMIC	WGS	RANDOM	447	A59238	SRX2238884	"WGS analysis of normal sample TARGET-15-PAREAT-15A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-PAREAT-15A-01D A59238 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59238_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634846	@dbgap@:reads/SRP011999/SRS1761176/SRX2238884/SRR5634846/SRR5634846.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PAREAT-09A-01D_TARGET-15-PAREAT-15A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-PAREAT-09A-01D_TARGET-15-PAREAT-15A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PAREAT.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-PARUIF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARUIF-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARUIF-09A-01D	DNA	EFO	SRS1761113	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARUIF-09A-01D A59151 library	PAIRED	GENOMIC	WGS	RANDOM	470	A59151	SRX2238821	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PARUIF-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-PARUIF-09A-01D A59151 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59151_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634833	@dbgap@:reads/SRP011999/SRS1761113/SRX2238821/SRR5634833/SRR5634833.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-PARUIF.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PARUIF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARUIF-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARUIF-09A-01D	DNA	EFO	SRS1761113	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARUIF-09A-01D A59151 library	PAIRED	GENOMIC	WGS	RANDOM	470	A59151	SRX2238821	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PARUIF-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-PARUIF-09A-01D A59151 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59151_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634833	@dbgap@:reads/SRP011999/SRS1761113/SRX2238821/SRR5634833/SRR5634833.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-PARUIF-09A-01D.fusion.vcf	3						
TARGET-15-PARUIF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARUIF-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARUIF-09A-01D	DNA	EFO	SRS1761113	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARUIF-09A-01D A59151 library	PAIRED	GENOMIC	WGS	RANDOM	470	A59151	SRX2238821	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PARUIF-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-PARUIF-09A-01D A59151 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59151_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634833	@dbgap@:reads/SRP011999/SRS1761113/SRX2238821/SRR5634833/SRR5634833.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-PARUIF-09A-01D.indel.vcf	3						
TARGET-15-PARUIF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARUIF-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARUIF-09A-01D	DNA	EFO	SRS1761113	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARUIF-09A-01D A59151 library	PAIRED	GENOMIC	WGS	RANDOM	470	A59151	SRX2238821	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PARUIF-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-PARUIF-09A-01D A59151 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59151_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634833	@dbgap@:reads/SRP011999/SRS1761113/SRX2238821/SRR5634833/SRR5634833.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-PARUIF.quality_tagged.vcf	3						
TARGET-15-PARUIF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARUIF-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARUIF-09A-01D	DNA	EFO	SRS1761113	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARUIF-09A-01D A59151 library	PAIRED	GENOMIC	WGS	RANDOM	470	A59151	SRX2238821	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PARUIF-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-PARUIF-09A-01D A59151 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59151_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634833	@dbgap@:reads/SRP011999/SRS1761113/SRX2238821/SRR5634833/SRR5634833.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-PARUIF-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-PARUIF-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-PARUIF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARUIF-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARUIF-09A-01D	DNA	EFO	SRS1761113	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARUIF-09A-01D A59151 library	PAIRED	GENOMIC	WGS	RANDOM	470	A59151	SRX2238821	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PARUIF-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-PARUIF-09A-01D A59151 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59151_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634833	@dbgap@:reads/SRP011999/SRS1761113/SRX2238821/SRR5634833/SRR5634833.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PARUIF.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PARUIF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARUIF-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARUIF-09A-01D	DNA	EFO	SRS1761113	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARUIF-09A-01D A59151 library	PAIRED	GENOMIC	WGS	RANDOM	470	A59151	SRX2238821	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PARUIF-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-PARUIF-09A-01D A59151 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59151_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634833	@dbgap@:reads/SRP011999/SRS1761113/SRX2238821/SRR5634833/SRR5634833.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PARUIF-09A-01D_TARGET-15-PARUIF-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-PARUIF-09A-01D_TARGET-15-PARUIF-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-PARUIF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARUIF-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARUIF-09A-01D	DNA	EFO	SRS1761113	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARUIF-09A-01D A59151 library	PAIRED	GENOMIC	WGS	RANDOM	470	A59151	SRX2238821	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PARUIF-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-PARUIF-09A-01D A59151 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59151_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634833	@dbgap@:reads/SRP011999/SRS1761113/SRX2238821/SRR5634833/SRR5634833.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PARUIF-09A-01D_TARGET-15-PARUIF-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-PARUIF-09A-01D_TARGET-15-PARUIF-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PARUIF.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-PARUIF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARUIF-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARUIF-14A.1-01D	DNA	EFO	SRS1761147	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARUIF-14A.1-01D A59260 library	PAIRED	GENOMIC	WGS	RANDOM	428	A59260	SRX2238855	"WGS analysis of normal sample TARGET-15-PARUIF-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PARUIF-14A.1-01D A59260 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59260_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634865	@dbgap@:reads/SRP011999/SRS1761147/SRX2238855/SRR5634865/SRR5634865.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-PARUIF.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PARUIF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARUIF-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARUIF-14A.1-01D	DNA	EFO	SRS1761147	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARUIF-14A.1-01D A59260 library	PAIRED	GENOMIC	WGS	RANDOM	428	A59260	SRX2238855	"WGS analysis of normal sample TARGET-15-PARUIF-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PARUIF-14A.1-01D A59260 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59260_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634865	@dbgap@:reads/SRP011999/SRS1761147/SRX2238855/SRR5634865/SRR5634865.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-PARUIF.quality_tagged.vcf	3						
TARGET-15-PARUIF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARUIF-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARUIF-14A.1-01D	DNA	EFO	SRS1761147	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARUIF-14A.1-01D A59260 library	PAIRED	GENOMIC	WGS	RANDOM	428	A59260	SRX2238855	"WGS analysis of normal sample TARGET-15-PARUIF-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PARUIF-14A.1-01D A59260 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59260_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634865	@dbgap@:reads/SRP011999/SRS1761147/SRX2238855/SRR5634865/SRR5634865.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-PARUIF-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-PARUIF-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-PARUIF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARUIF-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARUIF-14A.1-01D	DNA	EFO	SRS1761147	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARUIF-14A.1-01D A59260 library	PAIRED	GENOMIC	WGS	RANDOM	428	A59260	SRX2238855	"WGS analysis of normal sample TARGET-15-PARUIF-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PARUIF-14A.1-01D A59260 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59260_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634865	@dbgap@:reads/SRP011999/SRS1761147/SRX2238855/SRR5634865/SRR5634865.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PARUIF.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PARUIF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARUIF-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARUIF-14A.1-01D	DNA	EFO	SRS1761147	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARUIF-14A.1-01D A59260 library	PAIRED	GENOMIC	WGS	RANDOM	428	A59260	SRX2238855	"WGS analysis of normal sample TARGET-15-PARUIF-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PARUIF-14A.1-01D A59260 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59260_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634865	@dbgap@:reads/SRP011999/SRS1761147/SRX2238855/SRR5634865/SRR5634865.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PARUIF-09A-01D_TARGET-15-PARUIF-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-PARUIF-09A-01D_TARGET-15-PARUIF-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-PARUIF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARUIF-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARUIF-14A.1-01D	DNA	EFO	SRS1761147	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARUIF-14A.1-01D A59260 library	PAIRED	GENOMIC	WGS	RANDOM	428	A59260	SRX2238855	"WGS analysis of normal sample TARGET-15-PARUIF-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PARUIF-14A.1-01D A59260 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59260_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634865	@dbgap@:reads/SRP011999/SRS1761147/SRX2238855/SRR5634865/SRR5634865.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PARUIF-09A-01D_TARGET-15-PARUIF-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-PARUIF-09A-01D_TARGET-15-PARUIF-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PARUIF.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-PARWPU	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARWPU-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARWPU-09A-01D	DNA	EFO	SRS1761137	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARWPU-09A-01D A59164 library	PAIRED	GENOMIC	WGS	RANDOM	482	A59164	SRX2238845	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PARWPU-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-PARWPU-09A-01D A59164 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59164_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634857	@dbgap@:reads/SRP011999/SRS1761137/SRX2238845/SRR5634857/SRR5634857.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-PARWPU.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PARWPU	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARWPU-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARWPU-09A-01D	DNA	EFO	SRS1761137	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARWPU-09A-01D A59164 library	PAIRED	GENOMIC	WGS	RANDOM	482	A59164	SRX2238845	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PARWPU-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-PARWPU-09A-01D A59164 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59164_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634857	@dbgap@:reads/SRP011999/SRS1761137/SRX2238845/SRR5634857/SRR5634857.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-PARWPU-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-PARWPU.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-PARWPU	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARWPU-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARWPU-09A-01D	DNA	EFO	SRS1761137	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARWPU-09A-01D A59164 library	PAIRED	GENOMIC	WGS	RANDOM	482	A59164	SRX2238845	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PARWPU-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-PARWPU-09A-01D A59164 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59164_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634857	@dbgap@:reads/SRP011999/SRS1761137/SRX2238845/SRR5634857/SRR5634857.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-PARWPU-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-PARWPU.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-PARWPU	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARWPU-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARWPU-09A-01D	DNA	EFO	SRS1761137	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARWPU-09A-01D A59164 library	PAIRED	GENOMIC	WGS	RANDOM	482	A59164	SRX2238845	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PARWPU-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-PARWPU-09A-01D A59164 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59164_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634857	@dbgap@:reads/SRP011999/SRS1761137/SRX2238845/SRR5634857/SRR5634857.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-PARWPU-09A-01D.indel.vcf	3						
TARGET-15-PARWPU	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARWPU-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARWPU-09A-01D	DNA	EFO	SRS1761137	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARWPU-09A-01D A59164 library	PAIRED	GENOMIC	WGS	RANDOM	482	A59164	SRX2238845	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PARWPU-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-PARWPU-09A-01D A59164 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59164_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634857	@dbgap@:reads/SRP011999/SRS1761137/SRX2238845/SRR5634857/SRR5634857.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-PARWPU.quality_tagged.vcf	3						
TARGET-15-PARWPU	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARWPU-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARWPU-09A-01D	DNA	EFO	SRS1761137	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARWPU-09A-01D A59164 library	PAIRED	GENOMIC	WGS	RANDOM	482	A59164	SRX2238845	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PARWPU-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-PARWPU-09A-01D A59164 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59164_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634857	@dbgap@:reads/SRP011999/SRS1761137/SRX2238845/SRR5634857/SRR5634857.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-PARWPU-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-PARWPU-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-PARWPU	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARWPU-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARWPU-09A-01D	DNA	EFO	SRS1761137	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARWPU-09A-01D A59164 library	PAIRED	GENOMIC	WGS	RANDOM	482	A59164	SRX2238845	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PARWPU-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-PARWPU-09A-01D A59164 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59164_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634857	@dbgap@:reads/SRP011999/SRS1761137/SRX2238845/SRR5634857/SRR5634857.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PARWPU.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PARWPU	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARWPU-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARWPU-09A-01D	DNA	EFO	SRS1761137	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARWPU-09A-01D A59164 library	PAIRED	GENOMIC	WGS	RANDOM	482	A59164	SRX2238845	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PARWPU-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-PARWPU-09A-01D A59164 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59164_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634857	@dbgap@:reads/SRP011999/SRS1761137/SRX2238845/SRR5634857/SRR5634857.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PARWPU-09A-01D_TARGET-15-PARWPU-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-PARWPU-09A-01D_TARGET-15-PARWPU-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-PARWPU	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARWPU-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARWPU-09A-01D	DNA	EFO	SRS1761137	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARWPU-09A-01D A59164 library	PAIRED	GENOMIC	WGS	RANDOM	482	A59164	SRX2238845	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PARWPU-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-PARWPU-09A-01D A59164 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59164_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634857	@dbgap@:reads/SRP011999/SRS1761137/SRX2238845/SRR5634857/SRR5634857.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PARWPU-09A-01D_TARGET-15-PARWPU-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-PARWPU-09A-01D_TARGET-15-PARWPU-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PARWPU.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-PARWPU	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARWPU-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARWPU-14A.1-01D	DNA	EFO	SRS1761126	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARWPU-14A.1-01D A59273 library	PAIRED	GENOMIC	WGS	RANDOM	424	A59273	SRX2238834	"WGS analysis of normal sample TARGET-15-PARWPU-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PARWPU-14A.1-01D A59273 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59273_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634829	@dbgap@:reads/SRP011999/SRS1761126/SRX2238834/SRR5634829/SRR5634829.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-PARWPU.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PARWPU	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARWPU-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARWPU-14A.1-01D	DNA	EFO	SRS1761126	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARWPU-14A.1-01D A59273 library	PAIRED	GENOMIC	WGS	RANDOM	424	A59273	SRX2238834	"WGS analysis of normal sample TARGET-15-PARWPU-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PARWPU-14A.1-01D A59273 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59273_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634829	@dbgap@:reads/SRP011999/SRS1761126/SRX2238834/SRR5634829/SRR5634829.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-PARWPU.quality_tagged.vcf	3						
TARGET-15-PARWPU	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARWPU-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARWPU-14A.1-01D	DNA	EFO	SRS1761126	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARWPU-14A.1-01D A59273 library	PAIRED	GENOMIC	WGS	RANDOM	424	A59273	SRX2238834	"WGS analysis of normal sample TARGET-15-PARWPU-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PARWPU-14A.1-01D A59273 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59273_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634829	@dbgap@:reads/SRP011999/SRS1761126/SRX2238834/SRR5634829/SRR5634829.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-PARWPU-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-PARWPU-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-PARWPU	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARWPU-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARWPU-14A.1-01D	DNA	EFO	SRS1761126	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARWPU-14A.1-01D A59273 library	PAIRED	GENOMIC	WGS	RANDOM	424	A59273	SRX2238834	"WGS analysis of normal sample TARGET-15-PARWPU-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PARWPU-14A.1-01D A59273 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59273_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634829	@dbgap@:reads/SRP011999/SRS1761126/SRX2238834/SRR5634829/SRR5634829.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PARWPU.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PARWPU	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARWPU-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARWPU-14A.1-01D	DNA	EFO	SRS1761126	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARWPU-14A.1-01D A59273 library	PAIRED	GENOMIC	WGS	RANDOM	424	A59273	SRX2238834	"WGS analysis of normal sample TARGET-15-PARWPU-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PARWPU-14A.1-01D A59273 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59273_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634829	@dbgap@:reads/SRP011999/SRS1761126/SRX2238834/SRR5634829/SRR5634829.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PARWPU-09A-01D_TARGET-15-PARWPU-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-PARWPU-09A-01D_TARGET-15-PARWPU-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-PARWPU	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PARWPU-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PARWPU-14A.1-01D	DNA	EFO	SRS1761126	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PARWPU-14A.1-01D A59273 library	PAIRED	GENOMIC	WGS	RANDOM	424	A59273	SRX2238834	"WGS analysis of normal sample TARGET-15-PARWPU-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PARWPU-14A.1-01D A59273 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59273_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634829	@dbgap@:reads/SRP011999/SRS1761126/SRX2238834/SRR5634829/SRR5634829.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PARWPU-09A-01D_TARGET-15-PARWPU-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-PARWPU-09A-01D_TARGET-15-PARWPU-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PARWPU.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-PASZVW	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PASZVW-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PASZVW-09A-01D	DNA	EFO	SRS1761102	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PASZVW-09A-01D A59153 library	PAIRED	GENOMIC	WGS	RANDOM	475	A59153	SRX2238810	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PASZVW-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-PASZVW-09A-01D A59153 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59153_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634827	@dbgap@:reads/SRP011999/SRS1761102/SRX2238810/SRR5634827/SRR5634827.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-PASZVW.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PASZVW	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PASZVW-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PASZVW-09A-01D	DNA	EFO	SRS1761102	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PASZVW-09A-01D A59153 library	PAIRED	GENOMIC	WGS	RANDOM	475	A59153	SRX2238810	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PASZVW-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-PASZVW-09A-01D A59153 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59153_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634827	@dbgap@:reads/SRP011999/SRS1761102/SRX2238810/SRR5634827/SRR5634827.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-PASZVW-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-PASZVW.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-PASZVW	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PASZVW-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PASZVW-09A-01D	DNA	EFO	SRS1761102	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PASZVW-09A-01D A59153 library	PAIRED	GENOMIC	WGS	RANDOM	475	A59153	SRX2238810	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PASZVW-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-PASZVW-09A-01D A59153 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59153_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634827	@dbgap@:reads/SRP011999/SRS1761102/SRX2238810/SRR5634827/SRR5634827.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-PASZVW-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-PASZVW.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-PASZVW	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PASZVW-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PASZVW-09A-01D	DNA	EFO	SRS1761102	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PASZVW-09A-01D A59153 library	PAIRED	GENOMIC	WGS	RANDOM	475	A59153	SRX2238810	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PASZVW-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-PASZVW-09A-01D A59153 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59153_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634827	@dbgap@:reads/SRP011999/SRS1761102/SRX2238810/SRR5634827/SRR5634827.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-PASZVW-09A-01D.indel.vcf	3						
TARGET-15-PASZVW	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PASZVW-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PASZVW-09A-01D	DNA	EFO	SRS1761102	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PASZVW-09A-01D A59153 library	PAIRED	GENOMIC	WGS	RANDOM	475	A59153	SRX2238810	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PASZVW-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-PASZVW-09A-01D A59153 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59153_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634827	@dbgap@:reads/SRP011999/SRS1761102/SRX2238810/SRR5634827/SRR5634827.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-PASZVW.quality_tagged.vcf	3						
TARGET-15-PASZVW	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PASZVW-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PASZVW-09A-01D	DNA	EFO	SRS1761102	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PASZVW-09A-01D A59153 library	PAIRED	GENOMIC	WGS	RANDOM	475	A59153	SRX2238810	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PASZVW-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-PASZVW-09A-01D A59153 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59153_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634827	@dbgap@:reads/SRP011999/SRS1761102/SRX2238810/SRR5634827/SRR5634827.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-PASZVW-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-PASZVW-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-PASZVW	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PASZVW-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PASZVW-09A-01D	DNA	EFO	SRS1761102	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PASZVW-09A-01D A59153 library	PAIRED	GENOMIC	WGS	RANDOM	475	A59153	SRX2238810	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PASZVW-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-PASZVW-09A-01D A59153 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59153_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634827	@dbgap@:reads/SRP011999/SRS1761102/SRX2238810/SRR5634827/SRR5634827.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PASZVW.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PASZVW	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PASZVW-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PASZVW-09A-01D	DNA	EFO	SRS1761102	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PASZVW-09A-01D A59153 library	PAIRED	GENOMIC	WGS	RANDOM	475	A59153	SRX2238810	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PASZVW-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-PASZVW-09A-01D A59153 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59153_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634827	@dbgap@:reads/SRP011999/SRS1761102/SRX2238810/SRR5634827/SRR5634827.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PASZVW-09A-01D_TARGET-15-PASZVW-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-PASZVW-09A-01D_TARGET-15-PASZVW-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-PASZVW	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PASZVW-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PASZVW-09A-01D	DNA	EFO	SRS1761102	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PASZVW-09A-01D A59153 library	PAIRED	GENOMIC	WGS	RANDOM	475	A59153	SRX2238810	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PASZVW-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-PASZVW-09A-01D A59153 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59153_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634827	@dbgap@:reads/SRP011999/SRS1761102/SRX2238810/SRR5634827/SRR5634827.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PASZVW-09A-01D_TARGET-15-PASZVW-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-PASZVW-09A-01D_TARGET-15-PASZVW-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PASZVW.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-PASZVW	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PASZVW-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PASZVW-14A.1-01D	DNA	EFO	SRS1761191	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PASZVW-14A.1-01D A59262 library	PAIRED	GENOMIC	WGS	RANDOM	415	A59262	SRX2238899	"WGS analysis of normal sample TARGET-15-PASZVW-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PASZVW-14A.1-01D A59262 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59262_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634867	@dbgap@:reads/SRP011999/SRS1761191/SRX2238899/SRR5634867/SRR5634867.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-PASZVW.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PASZVW	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PASZVW-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PASZVW-14A.1-01D	DNA	EFO	SRS1761191	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PASZVW-14A.1-01D A59262 library	PAIRED	GENOMIC	WGS	RANDOM	415	A59262	SRX2238899	"WGS analysis of normal sample TARGET-15-PASZVW-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PASZVW-14A.1-01D A59262 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59262_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634867	@dbgap@:reads/SRP011999/SRS1761191/SRX2238899/SRR5634867/SRR5634867.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-PASZVW.quality_tagged.vcf	3						
TARGET-15-PASZVW	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PASZVW-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PASZVW-14A.1-01D	DNA	EFO	SRS1761191	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PASZVW-14A.1-01D A59262 library	PAIRED	GENOMIC	WGS	RANDOM	415	A59262	SRX2238899	"WGS analysis of normal sample TARGET-15-PASZVW-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PASZVW-14A.1-01D A59262 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59262_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634867	@dbgap@:reads/SRP011999/SRS1761191/SRX2238899/SRR5634867/SRR5634867.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-PASZVW-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-PASZVW-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-PASZVW	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PASZVW-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PASZVW-14A.1-01D	DNA	EFO	SRS1761191	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PASZVW-14A.1-01D A59262 library	PAIRED	GENOMIC	WGS	RANDOM	415	A59262	SRX2238899	"WGS analysis of normal sample TARGET-15-PASZVW-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PASZVW-14A.1-01D A59262 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59262_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634867	@dbgap@:reads/SRP011999/SRS1761191/SRX2238899/SRR5634867/SRR5634867.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PASZVW.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PASZVW	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PASZVW-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PASZVW-14A.1-01D	DNA	EFO	SRS1761191	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PASZVW-14A.1-01D A59262 library	PAIRED	GENOMIC	WGS	RANDOM	415	A59262	SRX2238899	"WGS analysis of normal sample TARGET-15-PASZVW-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PASZVW-14A.1-01D A59262 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59262_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634867	@dbgap@:reads/SRP011999/SRS1761191/SRX2238899/SRR5634867/SRR5634867.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PASZVW-09A-01D_TARGET-15-PASZVW-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-PASZVW-09A-01D_TARGET-15-PASZVW-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-PASZVW	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PASZVW-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PASZVW-14A.1-01D	DNA	EFO	SRS1761191	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PASZVW-14A.1-01D A59262 library	PAIRED	GENOMIC	WGS	RANDOM	415	A59262	SRX2238899	"WGS analysis of normal sample TARGET-15-PASZVW-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PASZVW-14A.1-01D A59262 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59262_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634867	@dbgap@:reads/SRP011999/SRS1761191/SRX2238899/SRR5634867/SRR5634867.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PASZVW-09A-01D_TARGET-15-PASZVW-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-PASZVW-09A-01D_TARGET-15-PASZVW-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PASZVW.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-PAUFIB	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAUFIB-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAUFIB-09A-01D	DNA	EFO	SRS1761195	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAUFIB-09A-01D A59154 library	PAIRED	GENOMIC	WGS	RANDOM	485	A59154	SRX2238903	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAUFIB-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-PAUFIB-09A-01D A59154 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59154_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634844	@dbgap@:reads/SRP011999/SRS1761195/SRX2238903/SRR5634844/SRR5634844.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-PAUFIB.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PAUFIB	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAUFIB-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAUFIB-09A-01D	DNA	EFO	SRS1761195	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAUFIB-09A-01D A59154 library	PAIRED	GENOMIC	WGS	RANDOM	485	A59154	SRX2238903	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAUFIB-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-PAUFIB-09A-01D A59154 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59154_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634844	@dbgap@:reads/SRP011999/SRS1761195/SRX2238903/SRR5634844/SRR5634844.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-PAUFIB-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-PAUFIB.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-PAUFIB	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAUFIB-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAUFIB-09A-01D	DNA	EFO	SRS1761195	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAUFIB-09A-01D A59154 library	PAIRED	GENOMIC	WGS	RANDOM	485	A59154	SRX2238903	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAUFIB-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-PAUFIB-09A-01D A59154 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59154_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634844	@dbgap@:reads/SRP011999/SRS1761195/SRX2238903/SRR5634844/SRR5634844.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-PAUFIB-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-PAUFIB.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-PAUFIB	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAUFIB-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAUFIB-09A-01D	DNA	EFO	SRS1761195	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAUFIB-09A-01D A59154 library	PAIRED	GENOMIC	WGS	RANDOM	485	A59154	SRX2238903	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAUFIB-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-PAUFIB-09A-01D A59154 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59154_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634844	@dbgap@:reads/SRP011999/SRS1761195/SRX2238903/SRR5634844/SRR5634844.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-PAUFIB-09A-01D.indel.vcf	3						
TARGET-15-PAUFIB	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAUFIB-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAUFIB-09A-01D	DNA	EFO	SRS1761195	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAUFIB-09A-01D A59154 library	PAIRED	GENOMIC	WGS	RANDOM	485	A59154	SRX2238903	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAUFIB-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-PAUFIB-09A-01D A59154 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59154_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634844	@dbgap@:reads/SRP011999/SRS1761195/SRX2238903/SRR5634844/SRR5634844.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-PAUFIB.quality_tagged.vcf	3						
TARGET-15-PAUFIB	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAUFIB-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAUFIB-09A-01D	DNA	EFO	SRS1761195	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAUFIB-09A-01D A59154 library	PAIRED	GENOMIC	WGS	RANDOM	485	A59154	SRX2238903	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAUFIB-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-PAUFIB-09A-01D A59154 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59154_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634844	@dbgap@:reads/SRP011999/SRS1761195/SRX2238903/SRR5634844/SRR5634844.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-PAUFIB-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-PAUFIB-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-PAUFIB	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAUFIB-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAUFIB-09A-01D	DNA	EFO	SRS1761195	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAUFIB-09A-01D A59154 library	PAIRED	GENOMIC	WGS	RANDOM	485	A59154	SRX2238903	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAUFIB-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-PAUFIB-09A-01D A59154 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59154_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634844	@dbgap@:reads/SRP011999/SRS1761195/SRX2238903/SRR5634844/SRR5634844.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PAUFIB.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PAUFIB	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAUFIB-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAUFIB-09A-01D	DNA	EFO	SRS1761195	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAUFIB-09A-01D A59154 library	PAIRED	GENOMIC	WGS	RANDOM	485	A59154	SRX2238903	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAUFIB-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-PAUFIB-09A-01D A59154 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59154_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634844	@dbgap@:reads/SRP011999/SRS1761195/SRX2238903/SRR5634844/SRR5634844.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PAUFIB-09A-01D_TARGET-15-PAUFIB-15A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-PAUFIB-09A-01D_TARGET-15-PAUFIB-15A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-PAUFIB	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAUFIB-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAUFIB-09A-01D	DNA	EFO	SRS1761195	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAUFIB-09A-01D A59154 library	PAIRED	GENOMIC	WGS	RANDOM	485	A59154	SRX2238903	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAUFIB-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-PAUFIB-09A-01D A59154 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59154_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634844	@dbgap@:reads/SRP011999/SRS1761195/SRX2238903/SRR5634844/SRR5634844.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PAUFIB-09A-01D_TARGET-15-PAUFIB-15A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-PAUFIB-09A-01D_TARGET-15-PAUFIB-15A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PAUFIB.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-PAUFIB	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAUFIB-15A	organism part	EFO	Bone Marrow	NCIt	"Fibroblasts from Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAUFIB-15A-01D	DNA	EFO	SRS1761185	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAUFIB-15A-01D A59263 library	PAIRED	GENOMIC	WGS	RANDOM	451	A59263	SRX2238892	"WGS analysis of normal sample TARGET-15-PAUFIB-15A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PAUFIB-15A-01D A59263 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59263_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634837	@dbgap@:reads/SRP011999/SRS1761185/SRX2238892/SRR5634837/SRR5634837.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-PAUFIB.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PAUFIB	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAUFIB-15A	organism part	EFO	Bone Marrow	NCIt	"Fibroblasts from Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAUFIB-15A-01D	DNA	EFO	SRS1761185	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAUFIB-15A-01D A59263 library	PAIRED	GENOMIC	WGS	RANDOM	451	A59263	SRX2238892	"WGS analysis of normal sample TARGET-15-PAUFIB-15A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PAUFIB-15A-01D A59263 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59263_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634837	@dbgap@:reads/SRP011999/SRS1761185/SRX2238892/SRR5634837/SRR5634837.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-PAUFIB.quality_tagged.vcf	3						
TARGET-15-PAUFIB	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAUFIB-15A	organism part	EFO	Bone Marrow	NCIt	"Fibroblasts from Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAUFIB-15A-01D	DNA	EFO	SRS1761185	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAUFIB-15A-01D A59263 library	PAIRED	GENOMIC	WGS	RANDOM	451	A59263	SRX2238892	"WGS analysis of normal sample TARGET-15-PAUFIB-15A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PAUFIB-15A-01D A59263 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59263_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634837	@dbgap@:reads/SRP011999/SRS1761185/SRX2238892/SRR5634837/SRR5634837.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-PAUFIB-15A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-PAUFIB-15A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-PAUFIB	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAUFIB-15A	organism part	EFO	Bone Marrow	NCIt	"Fibroblasts from Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAUFIB-15A-01D	DNA	EFO	SRS1761185	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAUFIB-15A-01D A59263 library	PAIRED	GENOMIC	WGS	RANDOM	451	A59263	SRX2238892	"WGS analysis of normal sample TARGET-15-PAUFIB-15A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PAUFIB-15A-01D A59263 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59263_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634837	@dbgap@:reads/SRP011999/SRS1761185/SRX2238892/SRR5634837/SRR5634837.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PAUFIB.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PAUFIB	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAUFIB-15A	organism part	EFO	Bone Marrow	NCIt	"Fibroblasts from Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAUFIB-15A-01D	DNA	EFO	SRS1761185	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAUFIB-15A-01D A59263 library	PAIRED	GENOMIC	WGS	RANDOM	451	A59263	SRX2238892	"WGS analysis of normal sample TARGET-15-PAUFIB-15A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PAUFIB-15A-01D A59263 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59263_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634837	@dbgap@:reads/SRP011999/SRS1761185/SRX2238892/SRR5634837/SRR5634837.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PAUFIB-09A-01D_TARGET-15-PAUFIB-15A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-PAUFIB-09A-01D_TARGET-15-PAUFIB-15A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-PAUFIB	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAUFIB-15A	organism part	EFO	Bone Marrow	NCIt	"Fibroblasts from Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAUFIB-15A-01D	DNA	EFO	SRS1761185	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAUFIB-15A-01D A59263 library	PAIRED	GENOMIC	WGS	RANDOM	451	A59263	SRX2238892	"WGS analysis of normal sample TARGET-15-PAUFIB-15A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PAUFIB-15A-01D A59263 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59263_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634837	@dbgap@:reads/SRP011999/SRS1761185/SRX2238892/SRR5634837/SRR5634837.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PAUFIB-09A-01D_TARGET-15-PAUFIB-15A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-PAUFIB-09A-01D_TARGET-15-PAUFIB-15A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PAUFIB.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-PAVFTF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAVFTF-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAVFTF-09A-01D	DNA	EFO	SRS1761177	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAVFTF-09A-01D A59155 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59155	SRX2238885	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAVFTF-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-PAVFTF-09A-01D A59155 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59155_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634863	@dbgap@:reads/SRP011999/SRS1761177/SRX2238885/SRR5634863/SRR5634863.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-PAVFTF.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PAVFTF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAVFTF-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAVFTF-09A-01D	DNA	EFO	SRS1761177	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAVFTF-09A-01D A59155 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59155	SRX2238885	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAVFTF-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-PAVFTF-09A-01D A59155 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59155_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634863	@dbgap@:reads/SRP011999/SRS1761177/SRX2238885/SRR5634863/SRR5634863.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-PAVFTF-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-PAVFTF.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-PAVFTF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAVFTF-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAVFTF-09A-01D	DNA	EFO	SRS1761177	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAVFTF-09A-01D A59155 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59155	SRX2238885	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAVFTF-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-PAVFTF-09A-01D A59155 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59155_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634863	@dbgap@:reads/SRP011999/SRS1761177/SRX2238885/SRR5634863/SRR5634863.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-PAVFTF-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-PAVFTF.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-PAVFTF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAVFTF-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAVFTF-09A-01D	DNA	EFO	SRS1761177	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAVFTF-09A-01D A59155 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59155	SRX2238885	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAVFTF-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-PAVFTF-09A-01D A59155 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59155_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634863	@dbgap@:reads/SRP011999/SRS1761177/SRX2238885/SRR5634863/SRR5634863.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-PAVFTF-09A-01D.indel.vcf	3						
TARGET-15-PAVFTF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAVFTF-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAVFTF-09A-01D	DNA	EFO	SRS1761177	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAVFTF-09A-01D A59155 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59155	SRX2238885	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAVFTF-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-PAVFTF-09A-01D A59155 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59155_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634863	@dbgap@:reads/SRP011999/SRS1761177/SRX2238885/SRR5634863/SRR5634863.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-PAVFTF.quality_tagged.vcf	3						
TARGET-15-PAVFTF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAVFTF-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAVFTF-09A-01D	DNA	EFO	SRS1761177	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAVFTF-09A-01D A59155 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59155	SRX2238885	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAVFTF-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-PAVFTF-09A-01D A59155 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59155_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634863	@dbgap@:reads/SRP011999/SRS1761177/SRX2238885/SRR5634863/SRR5634863.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-PAVFTF-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-PAVFTF-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-PAVFTF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAVFTF-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAVFTF-09A-01D	DNA	EFO	SRS1761177	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAVFTF-09A-01D A59155 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59155	SRX2238885	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAVFTF-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-PAVFTF-09A-01D A59155 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59155_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634863	@dbgap@:reads/SRP011999/SRS1761177/SRX2238885/SRR5634863/SRR5634863.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PAVFTF.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PAVFTF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAVFTF-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAVFTF-09A-01D	DNA	EFO	SRS1761177	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAVFTF-09A-01D A59155 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59155	SRX2238885	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAVFTF-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-PAVFTF-09A-01D A59155 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59155_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634863	@dbgap@:reads/SRP011999/SRS1761177/SRX2238885/SRR5634863/SRR5634863.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PAVFTF-09A-01D_TARGET-15-PAVFTF-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-PAVFTF-09A-01D_TARGET-15-PAVFTF-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-PAVFTF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAVFTF-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAVFTF-09A-01D	DNA	EFO	SRS1761177	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAVFTF-09A-01D A59155 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59155	SRX2238885	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-PAVFTF-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-PAVFTF-09A-01D A59155 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59155_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634863	@dbgap@:reads/SRP011999/SRS1761177/SRX2238885/SRR5634863/SRR5634863.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PAVFTF-09A-01D_TARGET-15-PAVFTF-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-PAVFTF-09A-01D_TARGET-15-PAVFTF-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PAVFTF.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-PAVFTF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAVFTF-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAVFTF-14A.1-01D	DNA	EFO	SRS1761149	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAVFTF-14A.1-01D A59264 library	PAIRED	GENOMIC	WGS	RANDOM	456	A59264	SRX2238857	"WGS analysis of normal sample TARGET-15-PAVFTF-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PAVFTF-14A.1-01D A59264 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59264_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634873	@dbgap@:reads/SRP011999/SRS1761149/SRX2238857/SRR5634873/SRR5634873.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-PAVFTF.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PAVFTF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAVFTF-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAVFTF-14A.1-01D	DNA	EFO	SRS1761149	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAVFTF-14A.1-01D A59264 library	PAIRED	GENOMIC	WGS	RANDOM	456	A59264	SRX2238857	"WGS analysis of normal sample TARGET-15-PAVFTF-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PAVFTF-14A.1-01D A59264 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59264_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634873	@dbgap@:reads/SRP011999/SRS1761149/SRX2238857/SRR5634873/SRR5634873.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-PAVFTF.quality_tagged.vcf	3						
TARGET-15-PAVFTF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAVFTF-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAVFTF-14A.1-01D	DNA	EFO	SRS1761149	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAVFTF-14A.1-01D A59264 library	PAIRED	GENOMIC	WGS	RANDOM	456	A59264	SRX2238857	"WGS analysis of normal sample TARGET-15-PAVFTF-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PAVFTF-14A.1-01D A59264 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59264_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634873	@dbgap@:reads/SRP011999/SRS1761149/SRX2238857/SRR5634873/SRR5634873.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-PAVFTF-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-PAVFTF-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-PAVFTF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAVFTF-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAVFTF-14A.1-01D	DNA	EFO	SRS1761149	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAVFTF-14A.1-01D A59264 library	PAIRED	GENOMIC	WGS	RANDOM	456	A59264	SRX2238857	"WGS analysis of normal sample TARGET-15-PAVFTF-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PAVFTF-14A.1-01D A59264 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59264_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634873	@dbgap@:reads/SRP011999/SRS1761149/SRX2238857/SRR5634873/SRR5634873.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PAVFTF.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-PAVFTF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAVFTF-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAVFTF-14A.1-01D	DNA	EFO	SRS1761149	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAVFTF-14A.1-01D A59264 library	PAIRED	GENOMIC	WGS	RANDOM	456	A59264	SRX2238857	"WGS analysis of normal sample TARGET-15-PAVFTF-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PAVFTF-14A.1-01D A59264 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59264_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634873	@dbgap@:reads/SRP011999/SRS1761149/SRX2238857/SRR5634873/SRR5634873.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PAVFTF-09A-01D_TARGET-15-PAVFTF-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-PAVFTF-09A-01D_TARGET-15-PAVFTF-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-PAVFTF	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-PAVFTF-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-PAVFTF-14A.1-01D	DNA	EFO	SRS1761149	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-PAVFTF-14A.1-01D A59264 library	PAIRED	GENOMIC	WGS	RANDOM	456	A59264	SRX2238857	"WGS analysis of normal sample TARGET-15-PAVFTF-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-PAVFTF-14A.1-01D A59264 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59264_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634873	@dbgap@:reads/SRP011999/SRS1761149/SRX2238857/SRR5634873/SRR5634873.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-PAVFTF-09A-01D_TARGET-15-PAVFTF-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-PAVFTF-09A-01D_TARGET-15-PAVFTF-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-PAVFTF.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL011914	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL011914-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL011914-09A-01D	DNA	EFO	SRS1761200	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL011914-09A-01D A59163 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59163	SRX2238908	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL011914-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL011914-09A-01D A59163 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59163_3_lanes_dupsFlagged_reheadered.bam	SRR4415891	@dbgap@:reads/SRP011999/SRS1761200/SRX2238908/SRR4415891/SRR4415891.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL011914.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL011914	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL011914-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL011914-09A-01D	DNA	EFO	SRS1761200	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL011914-09A-01D A59163 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59163	SRX2238908	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL011914-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL011914-09A-01D A59163 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59163_3_lanes_dupsFlagged_reheadered.bam	SRR4415891	@dbgap@:reads/SRP011999/SRS1761200/SRX2238908/SRR4415891/SRR4415891.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL011914-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL011914.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL011914	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL011914-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL011914-09A-01D	DNA	EFO	SRS1761200	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL011914-09A-01D A59163 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59163	SRX2238908	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL011914-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL011914-09A-01D A59163 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59163_3_lanes_dupsFlagged_reheadered.bam	SRR4415891	@dbgap@:reads/SRP011999/SRS1761200/SRX2238908/SRR4415891/SRR4415891.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL011914-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL011914.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL011914	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL011914-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL011914-09A-01D	DNA	EFO	SRS1761200	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL011914-09A-01D A59163 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59163	SRX2238908	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL011914-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL011914-09A-01D A59163 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59163_3_lanes_dupsFlagged_reheadered.bam	SRR4415891	@dbgap@:reads/SRP011999/SRS1761200/SRX2238908/SRR4415891/SRR4415891.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL011914-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL011914	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL011914-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL011914-09A-01D	DNA	EFO	SRS1761200	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL011914-09A-01D A59163 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59163	SRX2238908	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL011914-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL011914-09A-01D A59163 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59163_3_lanes_dupsFlagged_reheadered.bam	SRR4415891	@dbgap@:reads/SRP011999/SRS1761200/SRX2238908/SRR4415891/SRR4415891.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL011914.quality_tagged.vcf	3						
TARGET-15-SJMPAL011914	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL011914-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL011914-09A-01D	DNA	EFO	SRS1761200	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL011914-09A-01D A59163 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59163	SRX2238908	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL011914-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL011914-09A-01D A59163 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59163_3_lanes_dupsFlagged_reheadered.bam	SRR4415891	@dbgap@:reads/SRP011999/SRS1761200/SRX2238908/SRR4415891/SRR4415891.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL011914-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL011914-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL011914	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL011914-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL011914-09A-01D	DNA	EFO	SRS1761200	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL011914-09A-01D A59163 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59163	SRX2238908	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL011914-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL011914-09A-01D A59163 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59163_3_lanes_dupsFlagged_reheadered.bam	SRR4415891	@dbgap@:reads/SRP011999/SRS1761200/SRX2238908/SRR4415891/SRR4415891.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL011914.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL011914	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL011914-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL011914-09A-01D	DNA	EFO	SRS1761200	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL011914-09A-01D A59163 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59163	SRX2238908	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL011914-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL011914-09A-01D A59163 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59163_3_lanes_dupsFlagged_reheadered.bam	SRR4415891	@dbgap@:reads/SRP011999/SRS1761200/SRX2238908/SRR4415891/SRR4415891.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL011914-09A-01D_TARGET-15-SJMPAL011914-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL011914-09A-01D_TARGET-15-SJMPAL011914-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL011914	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL011914-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL011914-09A-01D	DNA	EFO	SRS1761200	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL011914-09A-01D A59163 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59163	SRX2238908	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL011914-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL011914-09A-01D A59163 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59163_3_lanes_dupsFlagged_reheadered.bam	SRR4415891	@dbgap@:reads/SRP011999/SRS1761200/SRX2238908/SRR4415891/SRR4415891.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL011914-09A-01D_TARGET-15-SJMPAL011914-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL011914-09A-01D_TARGET-15-SJMPAL011914-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL011914.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL011914	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL011914-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL011914-14A-01D	DNA	EFO	SRS1761121	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL011914-14A-01D A59272 library	PAIRED	GENOMIC	WGS	RANDOM	452	A59272	SRX2238829	"WGS analysis of normal sample TARGET-15-SJMPAL011914-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL011914-14A-01D A59272 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59272_2_lanes_dupsFlagged_reheadered.bam	SRR4415855	@dbgap@:reads/SRP011999/SRS1761121/SRX2238829/SRR4415855/SRR4415855.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL011914.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL011914	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL011914-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL011914-14A-01D	DNA	EFO	SRS1761121	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL011914-14A-01D A59272 library	PAIRED	GENOMIC	WGS	RANDOM	452	A59272	SRX2238829	"WGS analysis of normal sample TARGET-15-SJMPAL011914-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL011914-14A-01D A59272 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59272_2_lanes_dupsFlagged_reheadered.bam	SRR4415855	@dbgap@:reads/SRP011999/SRS1761121/SRX2238829/SRR4415855/SRR4415855.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL011914.quality_tagged.vcf	3						
TARGET-15-SJMPAL011914	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL011914-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL011914-14A-01D	DNA	EFO	SRS1761121	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL011914-14A-01D A59272 library	PAIRED	GENOMIC	WGS	RANDOM	452	A59272	SRX2238829	"WGS analysis of normal sample TARGET-15-SJMPAL011914-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL011914-14A-01D A59272 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59272_2_lanes_dupsFlagged_reheadered.bam	SRR4415855	@dbgap@:reads/SRP011999/SRS1761121/SRX2238829/SRR4415855/SRR4415855.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL011914-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL011914-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL011914	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL011914-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL011914-14A-01D	DNA	EFO	SRS1761121	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL011914-14A-01D A59272 library	PAIRED	GENOMIC	WGS	RANDOM	452	A59272	SRX2238829	"WGS analysis of normal sample TARGET-15-SJMPAL011914-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL011914-14A-01D A59272 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59272_2_lanes_dupsFlagged_reheadered.bam	SRR4415855	@dbgap@:reads/SRP011999/SRS1761121/SRX2238829/SRR4415855/SRR4415855.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL011914.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL011914	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL011914-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL011914-14A-01D	DNA	EFO	SRS1761121	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL011914-14A-01D A59272 library	PAIRED	GENOMIC	WGS	RANDOM	452	A59272	SRX2238829	"WGS analysis of normal sample TARGET-15-SJMPAL011914-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL011914-14A-01D A59272 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59272_2_lanes_dupsFlagged_reheadered.bam	SRR4415855	@dbgap@:reads/SRP011999/SRS1761121/SRX2238829/SRR4415855/SRR4415855.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL011914-09A-01D_TARGET-15-SJMPAL011914-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL011914-09A-01D_TARGET-15-SJMPAL011914-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL011914	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL011914-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL011914-14A-01D	DNA	EFO	SRS1761121	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL011914-14A-01D A59272 library	PAIRED	GENOMIC	WGS	RANDOM	452	A59272	SRX2238829	"WGS analysis of normal sample TARGET-15-SJMPAL011914-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL011914-14A-01D A59272 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59272_2_lanes_dupsFlagged_reheadered.bam	SRR4415855	@dbgap@:reads/SRP011999/SRS1761121/SRX2238829/SRR4415855/SRR4415855.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL011914-09A-01D_TARGET-15-SJMPAL011914-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL011914-09A-01D_TARGET-15-SJMPAL011914-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL011914.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL012419	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012419-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012419-09A.1-01D	DNA	EFO	SRS1761196	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012419-09A.1-01D A59152 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59152	SRX2238904	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012419-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-SJMPAL012419-09A.1-01D A59152 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59152_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634875	@dbgap@:reads/SRP011999/SRS1761196/SRX2238904/SRR5634875/SRR5634875.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL012419.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL012419	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012419-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012419-09A.1-01D	DNA	EFO	SRS1761196	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012419-09A.1-01D A59152 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59152	SRX2238904	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012419-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-SJMPAL012419-09A.1-01D A59152 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59152_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634875	@dbgap@:reads/SRP011999/SRS1761196/SRX2238904/SRR5634875/SRR5634875.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL012419-09A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL012419.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL012419	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012419-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012419-09A.1-01D	DNA	EFO	SRS1761196	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012419-09A.1-01D A59152 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59152	SRX2238904	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012419-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-SJMPAL012419-09A.1-01D A59152 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59152_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634875	@dbgap@:reads/SRP011999/SRS1761196/SRX2238904/SRR5634875/SRR5634875.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL012419-09A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL012419.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL012419	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012419-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012419-09A.1-01D	DNA	EFO	SRS1761196	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012419-09A.1-01D A59152 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59152	SRX2238904	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012419-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-SJMPAL012419-09A.1-01D A59152 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59152_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634875	@dbgap@:reads/SRP011999/SRS1761196/SRX2238904/SRR5634875/SRR5634875.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL012419-09A.1-01D.indel.vcf	3						
TARGET-15-SJMPAL012419	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012419-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012419-09A.1-01D	DNA	EFO	SRS1761196	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012419-09A.1-01D A59152 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59152	SRX2238904	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012419-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-SJMPAL012419-09A.1-01D A59152 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59152_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634875	@dbgap@:reads/SRP011999/SRS1761196/SRX2238904/SRR5634875/SRR5634875.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL012419.quality_tagged.vcf	3						
TARGET-15-SJMPAL012419	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012419-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012419-09A.1-01D	DNA	EFO	SRS1761196	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012419-09A.1-01D A59152 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59152	SRX2238904	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012419-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-SJMPAL012419-09A.1-01D A59152 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59152_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634875	@dbgap@:reads/SRP011999/SRS1761196/SRX2238904/SRR5634875/SRR5634875.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL012419-09A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL012419-09A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL012419	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012419-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012419-09A.1-01D	DNA	EFO	SRS1761196	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012419-09A.1-01D A59152 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59152	SRX2238904	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012419-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-SJMPAL012419-09A.1-01D A59152 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59152_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634875	@dbgap@:reads/SRP011999/SRS1761196/SRX2238904/SRR5634875/SRR5634875.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL012419.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL012419	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012419-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012419-09A.1-01D	DNA	EFO	SRS1761196	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012419-09A.1-01D A59152 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59152	SRX2238904	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012419-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-SJMPAL012419-09A.1-01D A59152 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59152_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634875	@dbgap@:reads/SRP011999/SRS1761196/SRX2238904/SRR5634875/SRR5634875.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL012419-09A.1-01D_TARGET-15-SJMPAL012419-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL012419-09A.1-01D_TARGET-15-SJMPAL012419-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL012419	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012419-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012419-09A.1-01D	DNA	EFO	SRS1761196	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012419-09A.1-01D A59152 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59152	SRX2238904	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012419-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-SJMPAL012419-09A.1-01D A59152 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59152_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634875	@dbgap@:reads/SRP011999/SRS1761196/SRX2238904/SRR5634875/SRR5634875.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL012419-09A.1-01D_TARGET-15-SJMPAL012419-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL012419-09A.1-01D_TARGET-15-SJMPAL012419-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL012419.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL012419	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012419-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012419-14A-01D	DNA	EFO	SRS1761130	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012419-14A-01D A59261 library	PAIRED	GENOMIC	WGS	RANDOM	438	A59261	SRX2238837	"WGS analysis of normal sample TARGET-15-SJMPAL012419-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL012419-14A-01D A59261 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59261_2_lanes_dupsFlagged_reheadered.bam	SRR4415904	@dbgap@:reads/SRP011999/SRS1761130/SRX2238837/SRR4415904/SRR4415904.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL012419.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL012419	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012419-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012419-14A-01D	DNA	EFO	SRS1761130	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012419-14A-01D A59261 library	PAIRED	GENOMIC	WGS	RANDOM	438	A59261	SRX2238837	"WGS analysis of normal sample TARGET-15-SJMPAL012419-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL012419-14A-01D A59261 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59261_2_lanes_dupsFlagged_reheadered.bam	SRR4415904	@dbgap@:reads/SRP011999/SRS1761130/SRX2238837/SRR4415904/SRR4415904.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL012419.quality_tagged.vcf	3						
TARGET-15-SJMPAL012419	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012419-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012419-14A-01D	DNA	EFO	SRS1761130	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012419-14A-01D A59261 library	PAIRED	GENOMIC	WGS	RANDOM	438	A59261	SRX2238837	"WGS analysis of normal sample TARGET-15-SJMPAL012419-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL012419-14A-01D A59261 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59261_2_lanes_dupsFlagged_reheadered.bam	SRR4415904	@dbgap@:reads/SRP011999/SRS1761130/SRX2238837/SRR4415904/SRR4415904.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL012419-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL012419-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL012419	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012419-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012419-14A-01D	DNA	EFO	SRS1761130	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012419-14A-01D A59261 library	PAIRED	GENOMIC	WGS	RANDOM	438	A59261	SRX2238837	"WGS analysis of normal sample TARGET-15-SJMPAL012419-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL012419-14A-01D A59261 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59261_2_lanes_dupsFlagged_reheadered.bam	SRR4415904	@dbgap@:reads/SRP011999/SRS1761130/SRX2238837/SRR4415904/SRR4415904.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL012419.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL012419	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012419-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012419-14A-01D	DNA	EFO	SRS1761130	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012419-14A-01D A59261 library	PAIRED	GENOMIC	WGS	RANDOM	438	A59261	SRX2238837	"WGS analysis of normal sample TARGET-15-SJMPAL012419-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL012419-14A-01D A59261 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59261_2_lanes_dupsFlagged_reheadered.bam	SRR4415904	@dbgap@:reads/SRP011999/SRS1761130/SRX2238837/SRR4415904/SRR4415904.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL012419-09A.1-01D_TARGET-15-SJMPAL012419-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL012419-09A.1-01D_TARGET-15-SJMPAL012419-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL012419	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012419-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012419-14A-01D	DNA	EFO	SRS1761130	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012419-14A-01D A59261 library	PAIRED	GENOMIC	WGS	RANDOM	438	A59261	SRX2238837	"WGS analysis of normal sample TARGET-15-SJMPAL012419-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL012419-14A-01D A59261 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59261_2_lanes_dupsFlagged_reheadered.bam	SRR4415904	@dbgap@:reads/SRP011999/SRS1761130/SRX2238837/SRR4415904/SRR4415904.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL012419-09A.1-01D_TARGET-15-SJMPAL012419-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL012419-09A.1-01D_TARGET-15-SJMPAL012419-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL012419.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL012421	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012421-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012421-09A-01D	DNA	EFO	SRS1761112	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012421-09A-01D A59126 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59126	SRX2238820	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012421-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL012421-09A-01D A59126 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59126_3_lanes_dupsFlagged_reheadered.bam	SRR4415887	@dbgap@:reads/SRP011999/SRS1761112/SRX2238820/SRR4415887/SRR4415887.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL012421.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL012421	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012421-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012421-09A-01D	DNA	EFO	SRS1761112	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012421-09A-01D A59126 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59126	SRX2238820	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012421-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL012421-09A-01D A59126 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59126_3_lanes_dupsFlagged_reheadered.bam	SRR4415887	@dbgap@:reads/SRP011999/SRS1761112/SRX2238820/SRR4415887/SRR4415887.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL012421-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL012421.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL012421	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012421-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012421-09A-01D	DNA	EFO	SRS1761112	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012421-09A-01D A59126 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59126	SRX2238820	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012421-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL012421-09A-01D A59126 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59126_3_lanes_dupsFlagged_reheadered.bam	SRR4415887	@dbgap@:reads/SRP011999/SRS1761112/SRX2238820/SRR4415887/SRR4415887.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL012421-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL012421.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL012421	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012421-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012421-09A-01D	DNA	EFO	SRS1761112	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012421-09A-01D A59126 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59126	SRX2238820	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012421-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL012421-09A-01D A59126 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59126_3_lanes_dupsFlagged_reheadered.bam	SRR4415887	@dbgap@:reads/SRP011999/SRS1761112/SRX2238820/SRR4415887/SRR4415887.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL012421-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL012421	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012421-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012421-09A-01D	DNA	EFO	SRS1761112	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012421-09A-01D A59126 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59126	SRX2238820	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012421-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL012421-09A-01D A59126 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59126_3_lanes_dupsFlagged_reheadered.bam	SRR4415887	@dbgap@:reads/SRP011999/SRS1761112/SRX2238820/SRR4415887/SRR4415887.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL012421.quality_tagged.vcf	3						
TARGET-15-SJMPAL012421	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012421-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012421-09A-01D	DNA	EFO	SRS1761112	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012421-09A-01D A59126 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59126	SRX2238820	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012421-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL012421-09A-01D A59126 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59126_3_lanes_dupsFlagged_reheadered.bam	SRR4415887	@dbgap@:reads/SRP011999/SRS1761112/SRX2238820/SRR4415887/SRR4415887.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL012421-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL012421-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL012421	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012421-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012421-09A-01D	DNA	EFO	SRS1761112	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012421-09A-01D A59126 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59126	SRX2238820	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012421-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL012421-09A-01D A59126 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59126_3_lanes_dupsFlagged_reheadered.bam	SRR4415887	@dbgap@:reads/SRP011999/SRS1761112/SRX2238820/SRR4415887/SRR4415887.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL012421.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL012421	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012421-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012421-09A-01D	DNA	EFO	SRS1761112	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012421-09A-01D A59126 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59126	SRX2238820	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012421-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL012421-09A-01D A59126 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59126_3_lanes_dupsFlagged_reheadered.bam	SRR4415887	@dbgap@:reads/SRP011999/SRS1761112/SRX2238820/SRR4415887/SRR4415887.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL012421-09A-01D_TARGET-15-SJMPAL012421-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL012421-09A-01D_TARGET-15-SJMPAL012421-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL012421	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012421-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012421-09A-01D	DNA	EFO	SRS1761112	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012421-09A-01D A59126 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59126	SRX2238820	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012421-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL012421-09A-01D A59126 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59126_3_lanes_dupsFlagged_reheadered.bam	SRR4415887	@dbgap@:reads/SRP011999/SRS1761112/SRX2238820/SRR4415887/SRR4415887.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL012421-09A-01D_TARGET-15-SJMPAL012421-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL012421-09A-01D_TARGET-15-SJMPAL012421-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL012421.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL012421	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012421-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012421-14A.1-01D	DNA	EFO	SRS1761198	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012421-14A.1-01D A59236 library	PAIRED	GENOMIC	WGS	RANDOM	421	A59236	SRX2238906	"WGS analysis of normal sample TARGET-15-SJMPAL012421-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL012421-14A.1-01D A59236 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59236_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634836	@dbgap@:reads/SRP011999/SRS1761198/SRX2238906/SRR5634836/SRR5634836.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL012421.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL012421	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012421-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012421-14A.1-01D	DNA	EFO	SRS1761198	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012421-14A.1-01D A59236 library	PAIRED	GENOMIC	WGS	RANDOM	421	A59236	SRX2238906	"WGS analysis of normal sample TARGET-15-SJMPAL012421-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL012421-14A.1-01D A59236 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59236_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634836	@dbgap@:reads/SRP011999/SRS1761198/SRX2238906/SRR5634836/SRR5634836.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL012421.quality_tagged.vcf	3						
TARGET-15-SJMPAL012421	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012421-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012421-14A.1-01D	DNA	EFO	SRS1761198	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012421-14A.1-01D A59236 library	PAIRED	GENOMIC	WGS	RANDOM	421	A59236	SRX2238906	"WGS analysis of normal sample TARGET-15-SJMPAL012421-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL012421-14A.1-01D A59236 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59236_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634836	@dbgap@:reads/SRP011999/SRS1761198/SRX2238906/SRR5634836/SRR5634836.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL012421-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL012421-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL012421	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012421-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012421-14A.1-01D	DNA	EFO	SRS1761198	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012421-14A.1-01D A59236 library	PAIRED	GENOMIC	WGS	RANDOM	421	A59236	SRX2238906	"WGS analysis of normal sample TARGET-15-SJMPAL012421-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL012421-14A.1-01D A59236 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59236_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634836	@dbgap@:reads/SRP011999/SRS1761198/SRX2238906/SRR5634836/SRR5634836.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL012421.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL012421	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012421-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012421-14A.1-01D	DNA	EFO	SRS1761198	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012421-14A.1-01D A59236 library	PAIRED	GENOMIC	WGS	RANDOM	421	A59236	SRX2238906	"WGS analysis of normal sample TARGET-15-SJMPAL012421-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL012421-14A.1-01D A59236 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59236_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634836	@dbgap@:reads/SRP011999/SRS1761198/SRX2238906/SRR5634836/SRR5634836.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL012421-09A-01D_TARGET-15-SJMPAL012421-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL012421-09A-01D_TARGET-15-SJMPAL012421-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL012421	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012421-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012421-14A.1-01D	DNA	EFO	SRS1761198	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012421-14A.1-01D A59236 library	PAIRED	GENOMIC	WGS	RANDOM	421	A59236	SRX2238906	"WGS analysis of normal sample TARGET-15-SJMPAL012421-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL012421-14A.1-01D A59236 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59236_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634836	@dbgap@:reads/SRP011999/SRS1761198/SRX2238906/SRR5634836/SRR5634836.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL012421-09A-01D_TARGET-15-SJMPAL012421-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL012421-09A-01D_TARGET-15-SJMPAL012421-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL012421.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL012426	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012426-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012426-09A-01D	DNA	EFO	SRS1761156	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012426-09A-01D A59149 library	PAIRED	GENOMIC	WGS	RANDOM	477	A59149	SRX2238864	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012426-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-SJMPAL012426-09A-01D A59149 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59149_3_lanes_dupsFlagged_reheadered.bam	SRR4415903	@dbgap@:reads/SRP011999/SRS1761156/SRX2238864/SRR4415903/SRR4415903.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL012426.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL012426	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012426-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012426-09A-01D	DNA	EFO	SRS1761156	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012426-09A-01D A59149 library	PAIRED	GENOMIC	WGS	RANDOM	477	A59149	SRX2238864	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012426-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-SJMPAL012426-09A-01D A59149 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59149_3_lanes_dupsFlagged_reheadered.bam	SRR4415903	@dbgap@:reads/SRP011999/SRS1761156/SRX2238864/SRR4415903/SRR4415903.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL012426-09A-01D.fusion.vcf	3						
TARGET-15-SJMPAL012426	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012426-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012426-09A-01D	DNA	EFO	SRS1761156	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012426-09A-01D A59149 library	PAIRED	GENOMIC	WGS	RANDOM	477	A59149	SRX2238864	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012426-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-SJMPAL012426-09A-01D A59149 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59149_3_lanes_dupsFlagged_reheadered.bam	SRR4415903	@dbgap@:reads/SRP011999/SRS1761156/SRX2238864/SRR4415903/SRR4415903.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL012426-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL012426	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012426-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012426-09A-01D	DNA	EFO	SRS1761156	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012426-09A-01D A59149 library	PAIRED	GENOMIC	WGS	RANDOM	477	A59149	SRX2238864	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012426-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-SJMPAL012426-09A-01D A59149 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59149_3_lanes_dupsFlagged_reheadered.bam	SRR4415903	@dbgap@:reads/SRP011999/SRS1761156/SRX2238864/SRR4415903/SRR4415903.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL012426.quality_tagged.vcf	3						
TARGET-15-SJMPAL012426	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012426-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012426-09A-01D	DNA	EFO	SRS1761156	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012426-09A-01D A59149 library	PAIRED	GENOMIC	WGS	RANDOM	477	A59149	SRX2238864	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012426-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-SJMPAL012426-09A-01D A59149 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59149_3_lanes_dupsFlagged_reheadered.bam	SRR4415903	@dbgap@:reads/SRP011999/SRS1761156/SRX2238864/SRR4415903/SRR4415903.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL012426-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL012426-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL012426	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012426-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012426-09A-01D	DNA	EFO	SRS1761156	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012426-09A-01D A59149 library	PAIRED	GENOMIC	WGS	RANDOM	477	A59149	SRX2238864	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012426-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-SJMPAL012426-09A-01D A59149 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59149_3_lanes_dupsFlagged_reheadered.bam	SRR4415903	@dbgap@:reads/SRP011999/SRS1761156/SRX2238864/SRR4415903/SRR4415903.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL012426.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL012426	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012426-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012426-09A-01D	DNA	EFO	SRS1761156	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012426-09A-01D A59149 library	PAIRED	GENOMIC	WGS	RANDOM	477	A59149	SRX2238864	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012426-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-SJMPAL012426-09A-01D A59149 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59149_3_lanes_dupsFlagged_reheadered.bam	SRR4415903	@dbgap@:reads/SRP011999/SRS1761156/SRX2238864/SRR4415903/SRR4415903.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL012426-09A-01D_TARGET-15-SJMPAL012426-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL012426-09A-01D_TARGET-15-SJMPAL012426-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL012426	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012426-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012426-09A-01D	DNA	EFO	SRS1761156	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012426-09A-01D A59149 library	PAIRED	GENOMIC	WGS	RANDOM	477	A59149	SRX2238864	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012426-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-29	TARGET-15-SJMPAL012426-09A-01D A59149 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59149_3_lanes_dupsFlagged_reheadered.bam	SRR4415903	@dbgap@:reads/SRP011999/SRS1761156/SRX2238864/SRR4415903/SRR4415903.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL012426-09A-01D_TARGET-15-SJMPAL012426-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL012426-09A-01D_TARGET-15-SJMPAL012426-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL012426.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL012426	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012426-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012426-14A-01D	DNA	EFO	SRS1761183	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012426-14A-01D A59258 library	PAIRED	GENOMIC	WGS	RANDOM	435	A59258	SRX2238891	"WGS analysis of normal sample TARGET-15-SJMPAL012426-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL012426-14A-01D A59258 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59258_2_lanes_dupsFlagged_reheadered.bam	SRR4415838	@dbgap@:reads/SRP011999/SRS1761183/SRX2238891/SRR4415838/SRR4415838.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL012426.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL012426	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012426-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012426-14A-01D	DNA	EFO	SRS1761183	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012426-14A-01D A59258 library	PAIRED	GENOMIC	WGS	RANDOM	435	A59258	SRX2238891	"WGS analysis of normal sample TARGET-15-SJMPAL012426-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL012426-14A-01D A59258 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59258_2_lanes_dupsFlagged_reheadered.bam	SRR4415838	@dbgap@:reads/SRP011999/SRS1761183/SRX2238891/SRR4415838/SRR4415838.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL012426.quality_tagged.vcf	3						
TARGET-15-SJMPAL012426	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012426-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012426-14A-01D	DNA	EFO	SRS1761183	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012426-14A-01D A59258 library	PAIRED	GENOMIC	WGS	RANDOM	435	A59258	SRX2238891	"WGS analysis of normal sample TARGET-15-SJMPAL012426-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL012426-14A-01D A59258 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59258_2_lanes_dupsFlagged_reheadered.bam	SRR4415838	@dbgap@:reads/SRP011999/SRS1761183/SRX2238891/SRR4415838/SRR4415838.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL012426-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL012426-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL012426	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012426-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012426-14A-01D	DNA	EFO	SRS1761183	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012426-14A-01D A59258 library	PAIRED	GENOMIC	WGS	RANDOM	435	A59258	SRX2238891	"WGS analysis of normal sample TARGET-15-SJMPAL012426-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL012426-14A-01D A59258 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59258_2_lanes_dupsFlagged_reheadered.bam	SRR4415838	@dbgap@:reads/SRP011999/SRS1761183/SRX2238891/SRR4415838/SRR4415838.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL012426.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL012426	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012426-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012426-14A-01D	DNA	EFO	SRS1761183	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012426-14A-01D A59258 library	PAIRED	GENOMIC	WGS	RANDOM	435	A59258	SRX2238891	"WGS analysis of normal sample TARGET-15-SJMPAL012426-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL012426-14A-01D A59258 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59258_2_lanes_dupsFlagged_reheadered.bam	SRR4415838	@dbgap@:reads/SRP011999/SRS1761183/SRX2238891/SRR4415838/SRR4415838.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL012426-09A-01D_TARGET-15-SJMPAL012426-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL012426-09A-01D_TARGET-15-SJMPAL012426-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL012426	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012426-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012426-14A-01D	DNA	EFO	SRS1761183	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012426-14A-01D A59258 library	PAIRED	GENOMIC	WGS	RANDOM	435	A59258	SRX2238891	"WGS analysis of normal sample TARGET-15-SJMPAL012426-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL012426-14A-01D A59258 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59258_2_lanes_dupsFlagged_reheadered.bam	SRR4415838	@dbgap@:reads/SRP011999/SRS1761183/SRX2238891/SRR4415838/SRR4415838.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL012426-09A-01D_TARGET-15-SJMPAL012426-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL012426-09A-01D_TARGET-15-SJMPAL012426-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL012426.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL012427	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012427-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012427-09A-01D	DNA	EFO	SRS1761108	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012427-09A-01D A59144 library	PAIRED	GENOMIC	WGS	RANDOM	462	A59144	SRX2238816	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012427-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL012427-09A-01D A59144 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59144_3_lanes_dupsFlagged_reheadered.bam	SRR4415848	@dbgap@:reads/SRP011999/SRS1761108/SRX2238816/SRR4415848/SRR4415848.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL012427.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL012427	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012427-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012427-09A-01D	DNA	EFO	SRS1761108	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012427-09A-01D A59144 library	PAIRED	GENOMIC	WGS	RANDOM	462	A59144	SRX2238816	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012427-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL012427-09A-01D A59144 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59144_3_lanes_dupsFlagged_reheadered.bam	SRR4415848	@dbgap@:reads/SRP011999/SRS1761108/SRX2238816/SRR4415848/SRR4415848.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL012427-09A-01D.fusion.vcf	3						
TARGET-15-SJMPAL012427	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012427-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012427-09A-01D	DNA	EFO	SRS1761108	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012427-09A-01D A59144 library	PAIRED	GENOMIC	WGS	RANDOM	462	A59144	SRX2238816	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012427-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL012427-09A-01D A59144 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59144_3_lanes_dupsFlagged_reheadered.bam	SRR4415848	@dbgap@:reads/SRP011999/SRS1761108/SRX2238816/SRR4415848/SRR4415848.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL012427-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL012427	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012427-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012427-09A-01D	DNA	EFO	SRS1761108	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012427-09A-01D A59144 library	PAIRED	GENOMIC	WGS	RANDOM	462	A59144	SRX2238816	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012427-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL012427-09A-01D A59144 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59144_3_lanes_dupsFlagged_reheadered.bam	SRR4415848	@dbgap@:reads/SRP011999/SRS1761108/SRX2238816/SRR4415848/SRR4415848.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL012427.quality_tagged.vcf	3						
TARGET-15-SJMPAL012427	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012427-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012427-09A-01D	DNA	EFO	SRS1761108	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012427-09A-01D A59144 library	PAIRED	GENOMIC	WGS	RANDOM	462	A59144	SRX2238816	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012427-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL012427-09A-01D A59144 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59144_3_lanes_dupsFlagged_reheadered.bam	SRR4415848	@dbgap@:reads/SRP011999/SRS1761108/SRX2238816/SRR4415848/SRR4415848.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL012427-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL012427-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL012427	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012427-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012427-09A-01D	DNA	EFO	SRS1761108	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012427-09A-01D A59144 library	PAIRED	GENOMIC	WGS	RANDOM	462	A59144	SRX2238816	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012427-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL012427-09A-01D A59144 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59144_3_lanes_dupsFlagged_reheadered.bam	SRR4415848	@dbgap@:reads/SRP011999/SRS1761108/SRX2238816/SRR4415848/SRR4415848.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL012427.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL012427	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012427-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012427-09A-01D	DNA	EFO	SRS1761108	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012427-09A-01D A59144 library	PAIRED	GENOMIC	WGS	RANDOM	462	A59144	SRX2238816	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012427-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL012427-09A-01D A59144 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59144_3_lanes_dupsFlagged_reheadered.bam	SRR4415848	@dbgap@:reads/SRP011999/SRS1761108/SRX2238816/SRR4415848/SRR4415848.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL012427-09A-01D_TARGET-15-SJMPAL012427-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL012427-09A-01D_TARGET-15-SJMPAL012427-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL012427	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012427-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012427-09A-01D	DNA	EFO	SRS1761108	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012427-09A-01D A59144 library	PAIRED	GENOMIC	WGS	RANDOM	462	A59144	SRX2238816	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL012427-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL012427-09A-01D A59144 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59144_3_lanes_dupsFlagged_reheadered.bam	SRR4415848	@dbgap@:reads/SRP011999/SRS1761108/SRX2238816/SRR4415848/SRR4415848.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL012427-09A-01D_TARGET-15-SJMPAL012427-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL012427-09A-01D_TARGET-15-SJMPAL012427-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL012427.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL012427	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012427-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012427-14A.1-01D	DNA	EFO	SRS1761165	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012427-14A.1-01D A59253 library	PAIRED	GENOMIC	WGS	RANDOM	430	A59253	SRX2238873	"WGS analysis of normal sample TARGET-15-SJMPAL012427-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL012427-14A.1-01D A59253 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59253_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634832	@dbgap@:reads/SRP011999/SRS1761165/SRX2238873/SRR5634832/SRR5634832.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL012427.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL012427	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012427-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012427-14A.1-01D	DNA	EFO	SRS1761165	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012427-14A.1-01D A59253 library	PAIRED	GENOMIC	WGS	RANDOM	430	A59253	SRX2238873	"WGS analysis of normal sample TARGET-15-SJMPAL012427-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL012427-14A.1-01D A59253 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59253_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634832	@dbgap@:reads/SRP011999/SRS1761165/SRX2238873/SRR5634832/SRR5634832.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL012427.quality_tagged.vcf	3						
TARGET-15-SJMPAL012427	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012427-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012427-14A.1-01D	DNA	EFO	SRS1761165	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012427-14A.1-01D A59253 library	PAIRED	GENOMIC	WGS	RANDOM	430	A59253	SRX2238873	"WGS analysis of normal sample TARGET-15-SJMPAL012427-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL012427-14A.1-01D A59253 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59253_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634832	@dbgap@:reads/SRP011999/SRS1761165/SRX2238873/SRR5634832/SRR5634832.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL012427-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL012427-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL012427	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012427-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012427-14A.1-01D	DNA	EFO	SRS1761165	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012427-14A.1-01D A59253 library	PAIRED	GENOMIC	WGS	RANDOM	430	A59253	SRX2238873	"WGS analysis of normal sample TARGET-15-SJMPAL012427-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL012427-14A.1-01D A59253 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59253_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634832	@dbgap@:reads/SRP011999/SRS1761165/SRX2238873/SRR5634832/SRR5634832.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL012427.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL012427	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012427-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012427-14A.1-01D	DNA	EFO	SRS1761165	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012427-14A.1-01D A59253 library	PAIRED	GENOMIC	WGS	RANDOM	430	A59253	SRX2238873	"WGS analysis of normal sample TARGET-15-SJMPAL012427-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL012427-14A.1-01D A59253 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59253_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634832	@dbgap@:reads/SRP011999/SRS1761165/SRX2238873/SRR5634832/SRR5634832.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL012427-09A-01D_TARGET-15-SJMPAL012427-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL012427-09A-01D_TARGET-15-SJMPAL012427-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL012427	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL012427-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL012427-14A.1-01D	DNA	EFO	SRS1761165	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL012427-14A.1-01D A59253 library	PAIRED	GENOMIC	WGS	RANDOM	430	A59253	SRX2238873	"WGS analysis of normal sample TARGET-15-SJMPAL012427-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL012427-14A.1-01D A59253 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59253_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634832	@dbgap@:reads/SRP011999/SRS1761165/SRX2238873/SRR5634832/SRR5634832.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL012427-09A-01D_TARGET-15-SJMPAL012427-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL012427-09A-01D_TARGET-15-SJMPAL012427-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL012427.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL016342	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL016342-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL016342-09A-01D	DNA	EFO	SRS1761141	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL016342-09A-01D A59165 library	PAIRED	GENOMIC	WGS	RANDOM	498	A59165	SRX2238849	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL016342-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL016342-09A-01D A59165 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59165_3_lanes_dupsFlagged_reheadered.bam	SRR4415847	@dbgap@:reads/SRP011999/SRS1761141/SRX2238849/SRR4415847/SRR4415847.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL016342.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL016342	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL016342-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL016342-09A-01D	DNA	EFO	SRS1761141	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL016342-09A-01D A59165 library	PAIRED	GENOMIC	WGS	RANDOM	498	A59165	SRX2238849	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL016342-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL016342-09A-01D A59165 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59165_3_lanes_dupsFlagged_reheadered.bam	SRR4415847	@dbgap@:reads/SRP011999/SRS1761141/SRX2238849/SRR4415847/SRR4415847.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL016342-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL016342.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL016342	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL016342-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL016342-09A-01D	DNA	EFO	SRS1761141	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL016342-09A-01D A59165 library	PAIRED	GENOMIC	WGS	RANDOM	498	A59165	SRX2238849	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL016342-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL016342-09A-01D A59165 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59165_3_lanes_dupsFlagged_reheadered.bam	SRR4415847	@dbgap@:reads/SRP011999/SRS1761141/SRX2238849/SRR4415847/SRR4415847.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL016342-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL016342.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL016342	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL016342-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL016342-09A-01D	DNA	EFO	SRS1761141	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL016342-09A-01D A59165 library	PAIRED	GENOMIC	WGS	RANDOM	498	A59165	SRX2238849	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL016342-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL016342-09A-01D A59165 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59165_3_lanes_dupsFlagged_reheadered.bam	SRR4415847	@dbgap@:reads/SRP011999/SRS1761141/SRX2238849/SRR4415847/SRR4415847.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL016342-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL016342	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL016342-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL016342-09A-01D	DNA	EFO	SRS1761141	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL016342-09A-01D A59165 library	PAIRED	GENOMIC	WGS	RANDOM	498	A59165	SRX2238849	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL016342-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL016342-09A-01D A59165 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59165_3_lanes_dupsFlagged_reheadered.bam	SRR4415847	@dbgap@:reads/SRP011999/SRS1761141/SRX2238849/SRR4415847/SRR4415847.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL016342.quality_tagged.vcf	3						
TARGET-15-SJMPAL016342	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL016342-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL016342-09A-01D	DNA	EFO	SRS1761141	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL016342-09A-01D A59165 library	PAIRED	GENOMIC	WGS	RANDOM	498	A59165	SRX2238849	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL016342-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL016342-09A-01D A59165 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59165_3_lanes_dupsFlagged_reheadered.bam	SRR4415847	@dbgap@:reads/SRP011999/SRS1761141/SRX2238849/SRR4415847/SRR4415847.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL016342-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL016342-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL016342	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL016342-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL016342-09A-01D	DNA	EFO	SRS1761141	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL016342-09A-01D A59165 library	PAIRED	GENOMIC	WGS	RANDOM	498	A59165	SRX2238849	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL016342-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL016342-09A-01D A59165 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59165_3_lanes_dupsFlagged_reheadered.bam	SRR4415847	@dbgap@:reads/SRP011999/SRS1761141/SRX2238849/SRR4415847/SRR4415847.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL016342.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL016342	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL016342-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL016342-09A-01D	DNA	EFO	SRS1761141	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL016342-09A-01D A59165 library	PAIRED	GENOMIC	WGS	RANDOM	498	A59165	SRX2238849	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL016342-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL016342-09A-01D A59165 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59165_3_lanes_dupsFlagged_reheadered.bam	SRR4415847	@dbgap@:reads/SRP011999/SRS1761141/SRX2238849/SRR4415847/SRR4415847.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL016342-09A-01D_TARGET-15-SJMPAL016342-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL016342-09A-01D_TARGET-15-SJMPAL016342-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL016342	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL016342-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL016342-09A-01D	DNA	EFO	SRS1761141	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL016342-09A-01D A59165 library	PAIRED	GENOMIC	WGS	RANDOM	498	A59165	SRX2238849	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL016342-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL016342-09A-01D A59165 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59165_3_lanes_dupsFlagged_reheadered.bam	SRR4415847	@dbgap@:reads/SRP011999/SRS1761141/SRX2238849/SRR4415847/SRR4415847.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL016342-09A-01D_TARGET-15-SJMPAL016342-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL016342-09A-01D_TARGET-15-SJMPAL016342-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL016342.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL016342	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL016342-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL016342-14A.1-01D	DNA	EFO	SRS1761127	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL016342-14A.1-01D A59274 library	PAIRED	GENOMIC	WGS	RANDOM	432	A59274	SRX2238835	"WGS analysis of normal sample TARGET-15-SJMPAL016342-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL016342-14A.1-01D A59274 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59274_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634876	@dbgap@:reads/SRP011999/SRS1761127/SRX2238835/SRR5634876/SRR5634876.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL016342.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL016342	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL016342-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL016342-14A.1-01D	DNA	EFO	SRS1761127	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL016342-14A.1-01D A59274 library	PAIRED	GENOMIC	WGS	RANDOM	432	A59274	SRX2238835	"WGS analysis of normal sample TARGET-15-SJMPAL016342-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL016342-14A.1-01D A59274 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59274_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634876	@dbgap@:reads/SRP011999/SRS1761127/SRX2238835/SRR5634876/SRR5634876.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL016342.quality_tagged.vcf	3						
TARGET-15-SJMPAL016342	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL016342-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL016342-14A.1-01D	DNA	EFO	SRS1761127	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL016342-14A.1-01D A59274 library	PAIRED	GENOMIC	WGS	RANDOM	432	A59274	SRX2238835	"WGS analysis of normal sample TARGET-15-SJMPAL016342-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL016342-14A.1-01D A59274 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59274_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634876	@dbgap@:reads/SRP011999/SRS1761127/SRX2238835/SRR5634876/SRR5634876.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL016342-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL016342-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL016342	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL016342-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL016342-14A.1-01D	DNA	EFO	SRS1761127	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL016342-14A.1-01D A59274 library	PAIRED	GENOMIC	WGS	RANDOM	432	A59274	SRX2238835	"WGS analysis of normal sample TARGET-15-SJMPAL016342-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL016342-14A.1-01D A59274 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59274_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634876	@dbgap@:reads/SRP011999/SRS1761127/SRX2238835/SRR5634876/SRR5634876.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL016342.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL016342	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL016342-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL016342-14A.1-01D	DNA	EFO	SRS1761127	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL016342-14A.1-01D A59274 library	PAIRED	GENOMIC	WGS	RANDOM	432	A59274	SRX2238835	"WGS analysis of normal sample TARGET-15-SJMPAL016342-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL016342-14A.1-01D A59274 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59274_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634876	@dbgap@:reads/SRP011999/SRS1761127/SRX2238835/SRR5634876/SRR5634876.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL016342-09A-01D_TARGET-15-SJMPAL016342-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL016342-09A-01D_TARGET-15-SJMPAL016342-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL016342	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL016342-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL016342-14A.1-01D	DNA	EFO	SRS1761127	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL016342-14A.1-01D A59274 library	PAIRED	GENOMIC	WGS	RANDOM	432	A59274	SRX2238835	"WGS analysis of normal sample TARGET-15-SJMPAL016342-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL016342-14A.1-01D A59274 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59274_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634876	@dbgap@:reads/SRP011999/SRS1761127/SRX2238835/SRR5634876/SRR5634876.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL016342-09A-01D_TARGET-15-SJMPAL016342-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL016342-09A-01D_TARGET-15-SJMPAL016342-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL016342.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL017975	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017975-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017975-03A-01D	DNA	EFO	SRS1761110	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017975-03A-01D A59156 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59156	SRX2238818	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017975-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-SJMPAL017975-03A-01D A59156 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59156_3_lanes_dupsFlagged_reheadered.bam	SRR4415876	@dbgap@:reads/SRP011999/SRS1761110/SRX2238818/SRR4415876/SRR4415876.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL017975.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL017975	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017975-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017975-03A-01D	DNA	EFO	SRS1761110	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017975-03A-01D A59156 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59156	SRX2238818	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017975-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-SJMPAL017975-03A-01D A59156 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59156_3_lanes_dupsFlagged_reheadered.bam	SRR4415876	@dbgap@:reads/SRP011999/SRS1761110/SRX2238818/SRR4415876/SRR4415876.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL017975-03A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL017975.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL017975	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017975-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017975-03A-01D	DNA	EFO	SRS1761110	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017975-03A-01D A59156 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59156	SRX2238818	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017975-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-SJMPAL017975-03A-01D A59156 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59156_3_lanes_dupsFlagged_reheadered.bam	SRR4415876	@dbgap@:reads/SRP011999/SRS1761110/SRX2238818/SRR4415876/SRR4415876.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL017975-03A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL017975.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL017975	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017975-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017975-03A-01D	DNA	EFO	SRS1761110	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017975-03A-01D A59156 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59156	SRX2238818	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017975-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-SJMPAL017975-03A-01D A59156 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59156_3_lanes_dupsFlagged_reheadered.bam	SRR4415876	@dbgap@:reads/SRP011999/SRS1761110/SRX2238818/SRR4415876/SRR4415876.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL017975-03A-01D.indel.vcf	3						
TARGET-15-SJMPAL017975	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017975-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017975-03A-01D	DNA	EFO	SRS1761110	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017975-03A-01D A59156 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59156	SRX2238818	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017975-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-SJMPAL017975-03A-01D A59156 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59156_3_lanes_dupsFlagged_reheadered.bam	SRR4415876	@dbgap@:reads/SRP011999/SRS1761110/SRX2238818/SRR4415876/SRR4415876.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL017975.quality_tagged.vcf	3						
TARGET-15-SJMPAL017975	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017975-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017975-03A-01D	DNA	EFO	SRS1761110	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017975-03A-01D A59156 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59156	SRX2238818	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017975-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-SJMPAL017975-03A-01D A59156 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59156_3_lanes_dupsFlagged_reheadered.bam	SRR4415876	@dbgap@:reads/SRP011999/SRS1761110/SRX2238818/SRR4415876/SRR4415876.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL017975-03A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL017975-03A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL017975	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017975-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017975-03A-01D	DNA	EFO	SRS1761110	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017975-03A-01D A59156 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59156	SRX2238818	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017975-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-SJMPAL017975-03A-01D A59156 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59156_3_lanes_dupsFlagged_reheadered.bam	SRR4415876	@dbgap@:reads/SRP011999/SRS1761110/SRX2238818/SRR4415876/SRR4415876.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL017975.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL017975	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017975-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017975-03A-01D	DNA	EFO	SRS1761110	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017975-03A-01D A59156 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59156	SRX2238818	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017975-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-SJMPAL017975-03A-01D A59156 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59156_3_lanes_dupsFlagged_reheadered.bam	SRR4415876	@dbgap@:reads/SRP011999/SRS1761110/SRX2238818/SRR4415876/SRR4415876.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL017975-03A-01D_TARGET-15-SJMPAL017975-10A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL017975-03A-01D_TARGET-15-SJMPAL017975-10A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL017975	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017975-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017975-03A-01D	DNA	EFO	SRS1761110	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017975-03A-01D A59156 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59156	SRX2238818	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017975-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-SJMPAL017975-03A-01D A59156 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59156_3_lanes_dupsFlagged_reheadered.bam	SRR4415876	@dbgap@:reads/SRP011999/SRS1761110/SRX2238818/SRR4415876/SRR4415876.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL017975-03A-01D_TARGET-15-SJMPAL017975-10A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL017975-03A-01D_TARGET-15-SJMPAL017975-10A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL017975.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL017975	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017975-10A.1	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017975-10A.1-01D	DNA	EFO	SRS1761173	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017975-10A.1-01D A59265 library	PAIRED	GENOMIC	WGS	RANDOM	432	A59265	SRX2238881	"WGS analysis of normal sample TARGET-15-SJMPAL017975-10A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL017975-10A.1-01D A59265 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59265_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634854	@dbgap@:reads/SRP011999/SRS1761173/SRX2238881/SRR5634854/SRR5634854.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL017975.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL017975	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017975-10A.1	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017975-10A.1-01D	DNA	EFO	SRS1761173	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017975-10A.1-01D A59265 library	PAIRED	GENOMIC	WGS	RANDOM	432	A59265	SRX2238881	"WGS analysis of normal sample TARGET-15-SJMPAL017975-10A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL017975-10A.1-01D A59265 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59265_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634854	@dbgap@:reads/SRP011999/SRS1761173/SRX2238881/SRR5634854/SRR5634854.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL017975.quality_tagged.vcf	3						
TARGET-15-SJMPAL017975	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017975-10A.1	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017975-10A.1-01D	DNA	EFO	SRS1761173	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017975-10A.1-01D A59265 library	PAIRED	GENOMIC	WGS	RANDOM	432	A59265	SRX2238881	"WGS analysis of normal sample TARGET-15-SJMPAL017975-10A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL017975-10A.1-01D A59265 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59265_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634854	@dbgap@:reads/SRP011999/SRS1761173/SRX2238881/SRR5634854/SRR5634854.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL017975-10A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL017975-10A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL017975	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017975-10A.1	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017975-10A.1-01D	DNA	EFO	SRS1761173	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017975-10A.1-01D A59265 library	PAIRED	GENOMIC	WGS	RANDOM	432	A59265	SRX2238881	"WGS analysis of normal sample TARGET-15-SJMPAL017975-10A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL017975-10A.1-01D A59265 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59265_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634854	@dbgap@:reads/SRP011999/SRS1761173/SRX2238881/SRR5634854/SRR5634854.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL017975.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL017975	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017975-10A.1	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017975-10A.1-01D	DNA	EFO	SRS1761173	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017975-10A.1-01D A59265 library	PAIRED	GENOMIC	WGS	RANDOM	432	A59265	SRX2238881	"WGS analysis of normal sample TARGET-15-SJMPAL017975-10A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL017975-10A.1-01D A59265 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59265_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634854	@dbgap@:reads/SRP011999/SRS1761173/SRX2238881/SRR5634854/SRR5634854.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL017975-03A-01D_TARGET-15-SJMPAL017975-10A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL017975-03A-01D_TARGET-15-SJMPAL017975-10A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL017975	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017975-10A.1	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017975-10A.1-01D	DNA	EFO	SRS1761173	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017975-10A.1-01D A59265 library	PAIRED	GENOMIC	WGS	RANDOM	432	A59265	SRX2238881	"WGS analysis of normal sample TARGET-15-SJMPAL017975-10A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL017975-10A.1-01D A59265 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59265_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634854	@dbgap@:reads/SRP011999/SRS1761173/SRX2238881/SRR5634854/SRR5634854.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL017975-03A-01D_TARGET-15-SJMPAL017975-10A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL017975-03A-01D_TARGET-15-SJMPAL017975-10A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL017975.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.1-01D	DNA	EFO	SRS1761122	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.1-01D A59172 library	PAIRED	GENOMIC	WGS	RANDOM	489	A59172	SRX2238830	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.1-01D A59172 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59172_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634840	@dbgap@:reads/SRP011999/SRS1761122/SRX2238830/SRR5634840/SRR5634840.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL017976.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.1-01D	DNA	EFO	SRS1761122	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.1-01D A59172 library	PAIRED	GENOMIC	WGS	RANDOM	489	A59172	SRX2238830	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.1-01D A59172 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59172_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634840	@dbgap@:reads/SRP011999/SRS1761122/SRX2238830/SRR5634840/SRR5634840.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL017976-09A.1-01D.fusion.vcf	3						
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.1-01D	DNA	EFO	SRS1761122	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.1-01D A59172 library	PAIRED	GENOMIC	WGS	RANDOM	489	A59172	SRX2238830	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.1-01D A59172 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59172_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634840	@dbgap@:reads/SRP011999/SRS1761122/SRX2238830/SRR5634840/SRR5634840.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL017976-09A.1-01D.indel.vcf	3						
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.1-01D	DNA	EFO	SRS1761122	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.1-01D A59172 library	PAIRED	GENOMIC	WGS	RANDOM	489	A59172	SRX2238830	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.1-01D A59172 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59172_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634840	@dbgap@:reads/SRP011999/SRS1761122/SRX2238830/SRR5634840/SRR5634840.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL017976.quality_tagged.vcf	3						
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.1-01D	DNA	EFO	SRS1761122	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.1-01D A59172 library	PAIRED	GENOMIC	WGS	RANDOM	489	A59172	SRX2238830	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.1-01D A59172 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59172_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634840	@dbgap@:reads/SRP011999/SRS1761122/SRX2238830/SRR5634840/SRR5634840.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL017976-09A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL017976-09A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.1-01D	DNA	EFO	SRS1761122	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.1-01D A59172 library	PAIRED	GENOMIC	WGS	RANDOM	489	A59172	SRX2238830	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.1-01D A59172 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59172_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634840	@dbgap@:reads/SRP011999/SRS1761122/SRX2238830/SRR5634840/SRR5634840.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL017976.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.1-01D	DNA	EFO	SRS1761122	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.1-01D A59172 library	PAIRED	GENOMIC	WGS	RANDOM	489	A59172	SRX2238830	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.1-01D A59172 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59172_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634840	@dbgap@:reads/SRP011999/SRS1761122/SRX2238830/SRR5634840/SRR5634840.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL017976-09A.1-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL017976-09A.1-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.1-01D	DNA	EFO	SRS1761122	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.1-01D A59172 library	PAIRED	GENOMIC	WGS	RANDOM	489	A59172	SRX2238830	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.1-01D A59172 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59172_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634840	@dbgap@:reads/SRP011999/SRS1761122/SRX2238830/SRR5634840/SRR5634840.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL017976-09A.1-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL017976-09A.1-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL017976.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.2-01D	DNA	EFO	SRS1761106	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.2-01D A59173 library	PAIRED	GENOMIC	WGS	RANDOM	464	A59173	SRX2238814	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.2-01D A59173 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59173_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634855	@dbgap@:reads/SRP011999/SRS1761106/SRX2238814/SRR5634855/SRR5634855.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL017976.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.2-01D	DNA	EFO	SRS1761106	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.2-01D A59173 library	PAIRED	GENOMIC	WGS	RANDOM	464	A59173	SRX2238814	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.2-01D A59173 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59173_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634855	@dbgap@:reads/SRP011999/SRS1761106/SRX2238814/SRR5634855/SRR5634855.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL017976-09A.2-01D.fusion.vcf	3						
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.2-01D	DNA	EFO	SRS1761106	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.2-01D A59173 library	PAIRED	GENOMIC	WGS	RANDOM	464	A59173	SRX2238814	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.2-01D A59173 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59173_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634855	@dbgap@:reads/SRP011999/SRS1761106/SRX2238814/SRR5634855/SRR5634855.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL017976-09A.2-01D.indel.vcf	3						
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.2-01D	DNA	EFO	SRS1761106	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.2-01D A59173 library	PAIRED	GENOMIC	WGS	RANDOM	464	A59173	SRX2238814	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.2-01D A59173 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59173_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634855	@dbgap@:reads/SRP011999/SRS1761106/SRX2238814/SRR5634855/SRR5634855.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL017976.quality_tagged.vcf	3						
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.2-01D	DNA	EFO	SRS1761106	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.2-01D A59173 library	PAIRED	GENOMIC	WGS	RANDOM	464	A59173	SRX2238814	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.2-01D A59173 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59173_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634855	@dbgap@:reads/SRP011999/SRS1761106/SRX2238814/SRR5634855/SRR5634855.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL017976-09A.2-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL017976-09A.2-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.2-01D	DNA	EFO	SRS1761106	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.2-01D A59173 library	PAIRED	GENOMIC	WGS	RANDOM	464	A59173	SRX2238814	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.2-01D A59173 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59173_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634855	@dbgap@:reads/SRP011999/SRS1761106/SRX2238814/SRR5634855/SRR5634855.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL017976.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.2-01D	DNA	EFO	SRS1761106	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.2-01D A59173 library	PAIRED	GENOMIC	WGS	RANDOM	464	A59173	SRX2238814	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.2-01D A59173 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59173_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634855	@dbgap@:reads/SRP011999/SRS1761106/SRX2238814/SRR5634855/SRR5634855.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL017976-09A.2-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL017976-09A.2-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.2-01D	DNA	EFO	SRS1761106	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.2-01D A59173 library	PAIRED	GENOMIC	WGS	RANDOM	464	A59173	SRX2238814	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.2-01D A59173 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59173_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634855	@dbgap@:reads/SRP011999/SRS1761106/SRX2238814/SRR5634855/SRR5634855.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL017976-09A.2-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL017976-09A.2-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL017976.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.3-01D	DNA	EFO	SRS1761187	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.3-01D A59174 library	PAIRED	GENOMIC	WGS	RANDOM	458	A59174	SRX2238894	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.3-01D A59174 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59174_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634830	@dbgap@:reads/SRP011999/SRS1761187/SRX2238894/SRR5634830/SRR5634830.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL017976.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.3-01D	DNA	EFO	SRS1761187	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.3-01D A59174 library	PAIRED	GENOMIC	WGS	RANDOM	458	A59174	SRX2238894	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.3-01D A59174 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59174_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634830	@dbgap@:reads/SRP011999/SRS1761187/SRX2238894/SRR5634830/SRR5634830.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL017976-09A.3-01D.fusion.vcf	3						
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.3-01D	DNA	EFO	SRS1761187	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.3-01D A59174 library	PAIRED	GENOMIC	WGS	RANDOM	458	A59174	SRX2238894	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.3-01D A59174 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59174_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634830	@dbgap@:reads/SRP011999/SRS1761187/SRX2238894/SRR5634830/SRR5634830.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL017976-09A.3-01D.indel.vcf	3						
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.3-01D	DNA	EFO	SRS1761187	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.3-01D A59174 library	PAIRED	GENOMIC	WGS	RANDOM	458	A59174	SRX2238894	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.3-01D A59174 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59174_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634830	@dbgap@:reads/SRP011999/SRS1761187/SRX2238894/SRR5634830/SRR5634830.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL017976.quality_tagged.vcf	3						
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.3-01D	DNA	EFO	SRS1761187	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.3-01D A59174 library	PAIRED	GENOMIC	WGS	RANDOM	458	A59174	SRX2238894	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.3-01D A59174 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59174_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634830	@dbgap@:reads/SRP011999/SRS1761187/SRX2238894/SRR5634830/SRR5634830.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL017976-09A.3-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL017976-09A.3-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.3-01D	DNA	EFO	SRS1761187	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.3-01D A59174 library	PAIRED	GENOMIC	WGS	RANDOM	458	A59174	SRX2238894	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.3-01D A59174 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59174_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634830	@dbgap@:reads/SRP011999/SRS1761187/SRX2238894/SRR5634830/SRR5634830.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL017976.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.3-01D	DNA	EFO	SRS1761187	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.3-01D A59174 library	PAIRED	GENOMIC	WGS	RANDOM	458	A59174	SRX2238894	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.3-01D A59174 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59174_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634830	@dbgap@:reads/SRP011999/SRS1761187/SRX2238894/SRR5634830/SRR5634830.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL017976-09A.3-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL017976-09A.3-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-09A.3-01D	DNA	EFO	SRS1761187	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-09A.3-01D A59174 library	PAIRED	GENOMIC	WGS	RANDOM	458	A59174	SRX2238894	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL017976-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL017976-09A.3-01D A59174 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59174_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634830	@dbgap@:reads/SRP011999/SRS1761187/SRX2238894/SRR5634830/SRR5634830.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL017976-09A.3-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL017976-09A.3-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL017976.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-10A	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-10A-01D	DNA	EFO	SRS1761150	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-10A-01D A59279 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59279	SRX2238859	"WGS analysis of normal sample TARGET-15-SJMPAL017976-10A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL017976-10A-01D A59279 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59279_2_lanes_dupsFlagged_reheadered.bam	SRR4415911	@dbgap@:reads/SRP011999/SRS1761150/SRX2238859/SRR4415911/SRR4415911.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL017976.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-10A	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-10A-01D	DNA	EFO	SRS1761150	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-10A-01D A59279 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59279	SRX2238859	"WGS analysis of normal sample TARGET-15-SJMPAL017976-10A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL017976-10A-01D A59279 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59279_2_lanes_dupsFlagged_reheadered.bam	SRR4415911	@dbgap@:reads/SRP011999/SRS1761150/SRX2238859/SRR4415911/SRR4415911.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL017976.quality_tagged.vcf	3						
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-10A	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-10A-01D	DNA	EFO	SRS1761150	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-10A-01D A59279 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59279	SRX2238859	"WGS analysis of normal sample TARGET-15-SJMPAL017976-10A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL017976-10A-01D A59279 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59279_2_lanes_dupsFlagged_reheadered.bam	SRR4415911	@dbgap@:reads/SRP011999/SRS1761150/SRX2238859/SRR4415911/SRR4415911.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL017976-10A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL017976-10A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-10A	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-10A-01D	DNA	EFO	SRS1761150	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-10A-01D A59279 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59279	SRX2238859	"WGS analysis of normal sample TARGET-15-SJMPAL017976-10A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL017976-10A-01D A59279 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59279_2_lanes_dupsFlagged_reheadered.bam	SRR4415911	@dbgap@:reads/SRP011999/SRS1761150/SRX2238859/SRR4415911/SRR4415911.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL017976.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-10A	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-10A-01D	DNA	EFO	SRS1761150	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-10A-01D A59279 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59279	SRX2238859	"WGS analysis of normal sample TARGET-15-SJMPAL017976-10A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL017976-10A-01D A59279 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59279_2_lanes_dupsFlagged_reheadered.bam	SRR4415911	@dbgap@:reads/SRP011999/SRS1761150/SRX2238859/SRR4415911/SRR4415911.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL017976-09A.1-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL017976-09A.1-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-10A	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-10A-01D	DNA	EFO	SRS1761150	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-10A-01D A59279 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59279	SRX2238859	"WGS analysis of normal sample TARGET-15-SJMPAL017976-10A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL017976-10A-01D A59279 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59279_2_lanes_dupsFlagged_reheadered.bam	SRR4415911	@dbgap@:reads/SRP011999/SRS1761150/SRX2238859/SRR4415911/SRR4415911.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL017976-09A.1-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL017976-09A.1-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL017976.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-10A	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-10A-01D	DNA	EFO	SRS1761150	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-10A-01D A59279 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59279	SRX2238859	"WGS analysis of normal sample TARGET-15-SJMPAL017976-10A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL017976-10A-01D A59279 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59279_2_lanes_dupsFlagged_reheadered.bam	SRR4415911	@dbgap@:reads/SRP011999/SRS1761150/SRX2238859/SRR4415911/SRR4415911.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL017976-09A.2-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL017976-09A.2-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-10A	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-10A-01D	DNA	EFO	SRS1761150	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-10A-01D A59279 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59279	SRX2238859	"WGS analysis of normal sample TARGET-15-SJMPAL017976-10A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL017976-10A-01D A59279 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59279_2_lanes_dupsFlagged_reheadered.bam	SRR4415911	@dbgap@:reads/SRP011999/SRS1761150/SRX2238859/SRR4415911/SRR4415911.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL017976-09A.2-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL017976-09A.2-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL017976.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-10A	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-10A-01D	DNA	EFO	SRS1761150	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-10A-01D A59279 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59279	SRX2238859	"WGS analysis of normal sample TARGET-15-SJMPAL017976-10A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL017976-10A-01D A59279 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59279_2_lanes_dupsFlagged_reheadered.bam	SRR4415911	@dbgap@:reads/SRP011999/SRS1761150/SRX2238859/SRR4415911/SRR4415911.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL017976-09A.3-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL017976-09A.3-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL017976	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL017976-10A	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL017976-10A-01D	DNA	EFO	SRS1761150	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL017976-10A-01D A59279 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59279	SRX2238859	"WGS analysis of normal sample TARGET-15-SJMPAL017976-10A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL017976-10A-01D A59279 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59279_2_lanes_dupsFlagged_reheadered.bam	SRR4415911	@dbgap@:reads/SRP011999/SRS1761150/SRX2238859/SRR4415911/SRR4415911.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL017976-09A.3-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL017976-09A.3-01D_TARGET-15-SJMPAL017976-10A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL017976.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL019076	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL019076-04A.1	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL019076-04A.1-01D	DNA	EFO	SRS1761136	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL019076-04A.1-01D A59133 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59133	SRX2238844	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL019076-04A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL019076-04A.1-01D A59133 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59133_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634877	@dbgap@:reads/SRP011999/SRS1761136/SRX2238844/SRR5634877/SRR5634877.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL019076.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL019076	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL019076-04A.1	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL019076-04A.1-01D	DNA	EFO	SRS1761136	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL019076-04A.1-01D A59133 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59133	SRX2238844	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL019076-04A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL019076-04A.1-01D A59133 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59133_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634877	@dbgap@:reads/SRP011999/SRS1761136/SRX2238844/SRR5634877/SRR5634877.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL019076-04A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL019076.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL019076	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL019076-04A.1	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL019076-04A.1-01D	DNA	EFO	SRS1761136	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL019076-04A.1-01D A59133 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59133	SRX2238844	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL019076-04A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL019076-04A.1-01D A59133 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59133_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634877	@dbgap@:reads/SRP011999/SRS1761136/SRX2238844/SRR5634877/SRR5634877.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL019076-04A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL019076.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL019076	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL019076-04A.1	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL019076-04A.1-01D	DNA	EFO	SRS1761136	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL019076-04A.1-01D A59133 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59133	SRX2238844	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL019076-04A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL019076-04A.1-01D A59133 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59133_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634877	@dbgap@:reads/SRP011999/SRS1761136/SRX2238844/SRR5634877/SRR5634877.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL019076-04A.1-01D.indel.vcf	3						
TARGET-15-SJMPAL019076	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL019076-04A.1	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL019076-04A.1-01D	DNA	EFO	SRS1761136	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL019076-04A.1-01D A59133 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59133	SRX2238844	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL019076-04A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL019076-04A.1-01D A59133 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59133_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634877	@dbgap@:reads/SRP011999/SRS1761136/SRX2238844/SRR5634877/SRR5634877.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL019076.quality_tagged.vcf	3						
TARGET-15-SJMPAL019076	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL019076-04A.1	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL019076-04A.1-01D	DNA	EFO	SRS1761136	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL019076-04A.1-01D A59133 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59133	SRX2238844	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL019076-04A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL019076-04A.1-01D A59133 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59133_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634877	@dbgap@:reads/SRP011999/SRS1761136/SRX2238844/SRR5634877/SRR5634877.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL019076-04A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL019076-04A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL019076	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL019076-04A.1	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL019076-04A.1-01D	DNA	EFO	SRS1761136	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL019076-04A.1-01D A59133 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59133	SRX2238844	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL019076-04A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL019076-04A.1-01D A59133 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59133_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634877	@dbgap@:reads/SRP011999/SRS1761136/SRX2238844/SRR5634877/SRR5634877.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL019076.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL019076	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL019076-04A.1	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL019076-04A.1-01D	DNA	EFO	SRS1761136	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL019076-04A.1-01D A59133 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59133	SRX2238844	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL019076-04A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL019076-04A.1-01D A59133 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59133_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634877	@dbgap@:reads/SRP011999/SRS1761136/SRX2238844/SRR5634877/SRR5634877.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL019076-04A.1-01D_TARGET-15-SJMPAL019076-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL019076-04A.1-01D_TARGET-15-SJMPAL019076-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL019076	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL019076-04A.1	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL019076-04A.1-01D	DNA	EFO	SRS1761136	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL019076-04A.1-01D A59133 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59133	SRX2238844	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL019076-04A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL019076-04A.1-01D A59133 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59133_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634877	@dbgap@:reads/SRP011999/SRS1761136/SRX2238844/SRR5634877/SRR5634877.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL019076-04A.1-01D_TARGET-15-SJMPAL019076-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL019076-04A.1-01D_TARGET-15-SJMPAL019076-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL019076.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL019076	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL019076-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL019076-14A-01D	DNA	EFO	SRS1761152	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL019076-14A-01D A59242 library	PAIRED	GENOMIC	WGS	RANDOM	448	A59242	SRX2238861	"WGS analysis of normal sample TARGET-15-SJMPAL019076-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL019076-14A-01D A59242 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59242_2_lanes_dupsFlagged_reheadered.bam	SRR4415927	@dbgap@:reads/SRP011999/SRS1761152/SRX2238861/SRR4415927/SRR4415927.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL019076.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL019076	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL019076-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL019076-14A-01D	DNA	EFO	SRS1761152	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL019076-14A-01D A59242 library	PAIRED	GENOMIC	WGS	RANDOM	448	A59242	SRX2238861	"WGS analysis of normal sample TARGET-15-SJMPAL019076-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL019076-14A-01D A59242 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59242_2_lanes_dupsFlagged_reheadered.bam	SRR4415927	@dbgap@:reads/SRP011999/SRS1761152/SRX2238861/SRR4415927/SRR4415927.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL019076.quality_tagged.vcf	3						
TARGET-15-SJMPAL019076	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL019076-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL019076-14A-01D	DNA	EFO	SRS1761152	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL019076-14A-01D A59242 library	PAIRED	GENOMIC	WGS	RANDOM	448	A59242	SRX2238861	"WGS analysis of normal sample TARGET-15-SJMPAL019076-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL019076-14A-01D A59242 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59242_2_lanes_dupsFlagged_reheadered.bam	SRR4415927	@dbgap@:reads/SRP011999/SRS1761152/SRX2238861/SRR4415927/SRR4415927.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL019076-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL019076-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL019076	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL019076-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL019076-14A-01D	DNA	EFO	SRS1761152	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL019076-14A-01D A59242 library	PAIRED	GENOMIC	WGS	RANDOM	448	A59242	SRX2238861	"WGS analysis of normal sample TARGET-15-SJMPAL019076-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL019076-14A-01D A59242 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59242_2_lanes_dupsFlagged_reheadered.bam	SRR4415927	@dbgap@:reads/SRP011999/SRS1761152/SRX2238861/SRR4415927/SRR4415927.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL019076.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL019076	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL019076-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL019076-14A-01D	DNA	EFO	SRS1761152	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL019076-14A-01D A59242 library	PAIRED	GENOMIC	WGS	RANDOM	448	A59242	SRX2238861	"WGS analysis of normal sample TARGET-15-SJMPAL019076-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL019076-14A-01D A59242 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59242_2_lanes_dupsFlagged_reheadered.bam	SRR4415927	@dbgap@:reads/SRP011999/SRS1761152/SRX2238861/SRR4415927/SRR4415927.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL019076-04A.1-01D_TARGET-15-SJMPAL019076-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL019076-04A.1-01D_TARGET-15-SJMPAL019076-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL019076	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL019076-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL019076-14A-01D	DNA	EFO	SRS1761152	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL019076-14A-01D A59242 library	PAIRED	GENOMIC	WGS	RANDOM	448	A59242	SRX2238861	"WGS analysis of normal sample TARGET-15-SJMPAL019076-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL019076-14A-01D A59242 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59242_2_lanes_dupsFlagged_reheadered.bam	SRR4415927	@dbgap@:reads/SRP011999/SRS1761152/SRX2238861/SRR4415927/SRR4415927.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL019076-04A.1-01D_TARGET-15-SJMPAL019076-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL019076-04A.1-01D_TARGET-15-SJMPAL019076-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL019076.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040025	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040025-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040025-09A-01D	DNA	EFO	SRS1761117	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040025-09A-01D A59157 library	PAIRED	GENOMIC	WGS	RANDOM	494	A59157	SRX2238825	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040025-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-SJMPAL040025-09A-01D A59157 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59157_3_lanes_dupsFlagged_reheadered.bam	SRR4415845	@dbgap@:reads/SRP011999/SRS1761117/SRX2238825/SRR4415845/SRR4415845.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040025.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040025	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040025-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040025-09A-01D	DNA	EFO	SRS1761117	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040025-09A-01D A59157 library	PAIRED	GENOMIC	WGS	RANDOM	494	A59157	SRX2238825	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040025-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-SJMPAL040025-09A-01D A59157 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59157_3_lanes_dupsFlagged_reheadered.bam	SRR4415845	@dbgap@:reads/SRP011999/SRS1761117/SRX2238825/SRR4415845/SRR4415845.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040025-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040025.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL040025	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040025-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040025-09A-01D	DNA	EFO	SRS1761117	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040025-09A-01D A59157 library	PAIRED	GENOMIC	WGS	RANDOM	494	A59157	SRX2238825	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040025-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-SJMPAL040025-09A-01D A59157 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59157_3_lanes_dupsFlagged_reheadered.bam	SRR4415845	@dbgap@:reads/SRP011999/SRS1761117/SRX2238825/SRR4415845/SRR4415845.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040025-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040025.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL040025	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040025-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040025-09A-01D	DNA	EFO	SRS1761117	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040025-09A-01D A59157 library	PAIRED	GENOMIC	WGS	RANDOM	494	A59157	SRX2238825	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040025-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-SJMPAL040025-09A-01D A59157 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59157_3_lanes_dupsFlagged_reheadered.bam	SRR4415845	@dbgap@:reads/SRP011999/SRS1761117/SRX2238825/SRR4415845/SRR4415845.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040025-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL040025	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040025-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040025-09A-01D	DNA	EFO	SRS1761117	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040025-09A-01D A59157 library	PAIRED	GENOMIC	WGS	RANDOM	494	A59157	SRX2238825	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040025-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-SJMPAL040025-09A-01D A59157 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59157_3_lanes_dupsFlagged_reheadered.bam	SRR4415845	@dbgap@:reads/SRP011999/SRS1761117/SRX2238825/SRR4415845/SRR4415845.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040025.quality_tagged.vcf	3						
TARGET-15-SJMPAL040025	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040025-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040025-09A-01D	DNA	EFO	SRS1761117	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040025-09A-01D A59157 library	PAIRED	GENOMIC	WGS	RANDOM	494	A59157	SRX2238825	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040025-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-SJMPAL040025-09A-01D A59157 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59157_3_lanes_dupsFlagged_reheadered.bam	SRR4415845	@dbgap@:reads/SRP011999/SRS1761117/SRX2238825/SRR4415845/SRR4415845.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040025-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040025-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040025	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040025-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040025-09A-01D	DNA	EFO	SRS1761117	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040025-09A-01D A59157 library	PAIRED	GENOMIC	WGS	RANDOM	494	A59157	SRX2238825	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040025-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-SJMPAL040025-09A-01D A59157 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59157_3_lanes_dupsFlagged_reheadered.bam	SRR4415845	@dbgap@:reads/SRP011999/SRS1761117/SRX2238825/SRR4415845/SRR4415845.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040025.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040025	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040025-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040025-09A-01D	DNA	EFO	SRS1761117	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040025-09A-01D A59157 library	PAIRED	GENOMIC	WGS	RANDOM	494	A59157	SRX2238825	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040025-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-SJMPAL040025-09A-01D A59157 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59157_3_lanes_dupsFlagged_reheadered.bam	SRR4415845	@dbgap@:reads/SRP011999/SRS1761117/SRX2238825/SRR4415845/SRR4415845.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040025-09A-01D_TARGET-15-SJMPAL040025-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040025-09A-01D_TARGET-15-SJMPAL040025-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040025	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040025-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040025-09A-01D	DNA	EFO	SRS1761117	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040025-09A-01D A59157 library	PAIRED	GENOMIC	WGS	RANDOM	494	A59157	SRX2238825	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040025-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-04	TARGET-15-SJMPAL040025-09A-01D A59157 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59157_3_lanes_dupsFlagged_reheadered.bam	SRR4415845	@dbgap@:reads/SRP011999/SRS1761117/SRX2238825/SRR4415845/SRR4415845.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040025-09A-01D_TARGET-15-SJMPAL040025-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040025-09A-01D_TARGET-15-SJMPAL040025-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040025.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040025	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040025-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040025-14A.1-01D	DNA	EFO	SRS1761124	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040025-14A.1-01D A59266 library	PAIRED	GENOMIC	WGS	RANDOM	432	A59266	SRX2238832	"WGS analysis of normal sample TARGET-15-SJMPAL040025-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040025-14A.1-01D A59266 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59266_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634871	@dbgap@:reads/SRP011999/SRS1761124/SRX2238832/SRR5634871/SRR5634871.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040025.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040025	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040025-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040025-14A.1-01D	DNA	EFO	SRS1761124	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040025-14A.1-01D A59266 library	PAIRED	GENOMIC	WGS	RANDOM	432	A59266	SRX2238832	"WGS analysis of normal sample TARGET-15-SJMPAL040025-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040025-14A.1-01D A59266 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59266_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634871	@dbgap@:reads/SRP011999/SRS1761124/SRX2238832/SRR5634871/SRR5634871.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040025.quality_tagged.vcf	3						
TARGET-15-SJMPAL040025	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040025-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040025-14A.1-01D	DNA	EFO	SRS1761124	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040025-14A.1-01D A59266 library	PAIRED	GENOMIC	WGS	RANDOM	432	A59266	SRX2238832	"WGS analysis of normal sample TARGET-15-SJMPAL040025-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040025-14A.1-01D A59266 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59266_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634871	@dbgap@:reads/SRP011999/SRS1761124/SRX2238832/SRR5634871/SRR5634871.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040025-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040025-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040025	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040025-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040025-14A.1-01D	DNA	EFO	SRS1761124	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040025-14A.1-01D A59266 library	PAIRED	GENOMIC	WGS	RANDOM	432	A59266	SRX2238832	"WGS analysis of normal sample TARGET-15-SJMPAL040025-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040025-14A.1-01D A59266 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59266_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634871	@dbgap@:reads/SRP011999/SRS1761124/SRX2238832/SRR5634871/SRR5634871.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040025.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040025	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040025-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040025-14A.1-01D	DNA	EFO	SRS1761124	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040025-14A.1-01D A59266 library	PAIRED	GENOMIC	WGS	RANDOM	432	A59266	SRX2238832	"WGS analysis of normal sample TARGET-15-SJMPAL040025-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040025-14A.1-01D A59266 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59266_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634871	@dbgap@:reads/SRP011999/SRS1761124/SRX2238832/SRR5634871/SRR5634871.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040025-09A-01D_TARGET-15-SJMPAL040025-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040025-09A-01D_TARGET-15-SJMPAL040025-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040025	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040025-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040025-14A.1-01D	DNA	EFO	SRS1761124	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040025-14A.1-01D A59266 library	PAIRED	GENOMIC	WGS	RANDOM	432	A59266	SRX2238832	"WGS analysis of normal sample TARGET-15-SJMPAL040025-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040025-14A.1-01D A59266 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59266_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634871	@dbgap@:reads/SRP011999/SRS1761124/SRX2238832/SRR5634871/SRR5634871.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040025-09A-01D_TARGET-15-SJMPAL040025-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040025-09A-01D_TARGET-15-SJMPAL040025-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040025.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.1	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.1-01D	DNA	EFO	SRS1761128	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.1-01D A59175 library	PAIRED	GENOMIC	WGS	RANDOM	492	A59175	SRX2238836	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.1-01D A59175 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59175_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634872	@dbgap@:reads/SRP011999/SRS1761128/SRX2238836/SRR5634872/SRR5634872.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040028.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.1	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.1-01D	DNA	EFO	SRS1761128	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.1-01D A59175 library	PAIRED	GENOMIC	WGS	RANDOM	492	A59175	SRX2238836	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.1-01D A59175 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59175_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634872	@dbgap@:reads/SRP011999/SRS1761128/SRX2238836/SRR5634872/SRR5634872.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040028-04A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040028.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.1	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.1-01D	DNA	EFO	SRS1761128	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.1-01D A59175 library	PAIRED	GENOMIC	WGS	RANDOM	492	A59175	SRX2238836	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.1-01D A59175 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59175_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634872	@dbgap@:reads/SRP011999/SRS1761128/SRX2238836/SRR5634872/SRR5634872.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040028-04A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040028.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.1	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.1-01D	DNA	EFO	SRS1761128	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.1-01D A59175 library	PAIRED	GENOMIC	WGS	RANDOM	492	A59175	SRX2238836	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.1-01D A59175 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59175_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634872	@dbgap@:reads/SRP011999/SRS1761128/SRX2238836/SRR5634872/SRR5634872.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040028-04A.1-01D.indel.vcf	3						
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.1	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.1-01D	DNA	EFO	SRS1761128	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.1-01D A59175 library	PAIRED	GENOMIC	WGS	RANDOM	492	A59175	SRX2238836	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.1-01D A59175 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59175_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634872	@dbgap@:reads/SRP011999/SRS1761128/SRX2238836/SRR5634872/SRR5634872.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040028.quality_tagged.vcf	3						
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.1	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.1-01D	DNA	EFO	SRS1761128	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.1-01D A59175 library	PAIRED	GENOMIC	WGS	RANDOM	492	A59175	SRX2238836	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.1-01D A59175 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59175_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634872	@dbgap@:reads/SRP011999/SRS1761128/SRX2238836/SRR5634872/SRR5634872.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040028-04A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040028-04A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.1	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.1-01D	DNA	EFO	SRS1761128	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.1-01D A59175 library	PAIRED	GENOMIC	WGS	RANDOM	492	A59175	SRX2238836	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.1-01D A59175 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59175_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634872	@dbgap@:reads/SRP011999/SRS1761128/SRX2238836/SRR5634872/SRR5634872.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040028.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.1	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.1-01D	DNA	EFO	SRS1761128	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.1-01D A59175 library	PAIRED	GENOMIC	WGS	RANDOM	492	A59175	SRX2238836	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.1-01D A59175 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59175_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634872	@dbgap@:reads/SRP011999/SRS1761128/SRX2238836/SRR5634872/SRR5634872.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040028-04A.1-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040028-04A.1-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.1	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.1-01D	DNA	EFO	SRS1761128	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.1-01D A59175 library	PAIRED	GENOMIC	WGS	RANDOM	492	A59175	SRX2238836	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.1-01D A59175 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59175_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634872	@dbgap@:reads/SRP011999/SRS1761128/SRX2238836/SRR5634872/SRR5634872.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040028-04A.1-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040028-04A.1-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040028.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.2	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.2-01D	DNA	EFO	SRS1761139	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.2-01D A59176 library	PAIRED	GENOMIC	WGS	RANDOM	483	A59176	SRX2238847	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.2-01D A59176 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59176_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634856	@dbgap@:reads/SRP011999/SRS1761139/SRX2238847/SRR5634856/SRR5634856.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040028.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.2	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.2-01D	DNA	EFO	SRS1761139	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.2-01D A59176 library	PAIRED	GENOMIC	WGS	RANDOM	483	A59176	SRX2238847	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.2-01D A59176 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59176_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634856	@dbgap@:reads/SRP011999/SRS1761139/SRX2238847/SRR5634856/SRR5634856.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040028-04A.2-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040028.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.2	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.2-01D	DNA	EFO	SRS1761139	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.2-01D A59176 library	PAIRED	GENOMIC	WGS	RANDOM	483	A59176	SRX2238847	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.2-01D A59176 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59176_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634856	@dbgap@:reads/SRP011999/SRS1761139/SRX2238847/SRR5634856/SRR5634856.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040028-04A.2-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040028.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.2	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.2-01D	DNA	EFO	SRS1761139	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.2-01D A59176 library	PAIRED	GENOMIC	WGS	RANDOM	483	A59176	SRX2238847	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.2-01D A59176 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59176_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634856	@dbgap@:reads/SRP011999/SRS1761139/SRX2238847/SRR5634856/SRR5634856.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040028-04A.2-01D.indel.vcf	3						
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.2	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.2-01D	DNA	EFO	SRS1761139	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.2-01D A59176 library	PAIRED	GENOMIC	WGS	RANDOM	483	A59176	SRX2238847	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.2-01D A59176 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59176_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634856	@dbgap@:reads/SRP011999/SRS1761139/SRX2238847/SRR5634856/SRR5634856.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040028.quality_tagged.vcf	3						
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.2	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.2-01D	DNA	EFO	SRS1761139	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.2-01D A59176 library	PAIRED	GENOMIC	WGS	RANDOM	483	A59176	SRX2238847	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.2-01D A59176 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59176_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634856	@dbgap@:reads/SRP011999/SRS1761139/SRX2238847/SRR5634856/SRR5634856.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040028-04A.2-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040028-04A.2-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.2	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.2-01D	DNA	EFO	SRS1761139	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.2-01D A59176 library	PAIRED	GENOMIC	WGS	RANDOM	483	A59176	SRX2238847	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.2-01D A59176 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59176_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634856	@dbgap@:reads/SRP011999/SRS1761139/SRX2238847/SRR5634856/SRR5634856.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040028.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.2	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.2-01D	DNA	EFO	SRS1761139	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.2-01D A59176 library	PAIRED	GENOMIC	WGS	RANDOM	483	A59176	SRX2238847	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.2-01D A59176 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59176_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634856	@dbgap@:reads/SRP011999/SRS1761139/SRX2238847/SRR5634856/SRR5634856.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040028-04A.2-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040028-04A.2-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.2	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.2-01D	DNA	EFO	SRS1761139	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.2-01D A59176 library	PAIRED	GENOMIC	WGS	RANDOM	483	A59176	SRX2238847	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.2-01D A59176 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59176_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634856	@dbgap@:reads/SRP011999/SRS1761139/SRX2238847/SRR5634856/SRR5634856.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040028-04A.2-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040028-04A.2-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040028.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.3	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.3-01D	DNA	EFO	SRS1761151	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.3-01D A59177 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59177	SRX2238858	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.3-01D A59177 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59177_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634862	@dbgap@:reads/SRP011999/SRS1761151/SRX2238858/SRR5634862/SRR5634862.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040028.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.3	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.3-01D	DNA	EFO	SRS1761151	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.3-01D A59177 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59177	SRX2238858	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.3-01D A59177 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59177_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634862	@dbgap@:reads/SRP011999/SRS1761151/SRX2238858/SRR5634862/SRR5634862.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040028-04A.3-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040028.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.3	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.3-01D	DNA	EFO	SRS1761151	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.3-01D A59177 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59177	SRX2238858	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.3-01D A59177 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59177_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634862	@dbgap@:reads/SRP011999/SRS1761151/SRX2238858/SRR5634862/SRR5634862.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040028-04A.3-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040028.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.3	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.3-01D	DNA	EFO	SRS1761151	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.3-01D A59177 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59177	SRX2238858	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.3-01D A59177 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59177_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634862	@dbgap@:reads/SRP011999/SRS1761151/SRX2238858/SRR5634862/SRR5634862.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040028-04A.3-01D.indel.vcf	3						
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.3	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.3-01D	DNA	EFO	SRS1761151	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.3-01D A59177 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59177	SRX2238858	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.3-01D A59177 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59177_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634862	@dbgap@:reads/SRP011999/SRS1761151/SRX2238858/SRR5634862/SRR5634862.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040028.quality_tagged.vcf	3						
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.3	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.3-01D	DNA	EFO	SRS1761151	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.3-01D A59177 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59177	SRX2238858	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.3-01D A59177 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59177_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634862	@dbgap@:reads/SRP011999/SRS1761151/SRX2238858/SRR5634862/SRR5634862.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040028-04A.3-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040028-04A.3-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.3	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.3-01D	DNA	EFO	SRS1761151	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.3-01D A59177 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59177	SRX2238858	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.3-01D A59177 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59177_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634862	@dbgap@:reads/SRP011999/SRS1761151/SRX2238858/SRR5634862/SRR5634862.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040028.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.3	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.3-01D	DNA	EFO	SRS1761151	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.3-01D A59177 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59177	SRX2238858	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.3-01D A59177 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59177_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634862	@dbgap@:reads/SRP011999/SRS1761151/SRX2238858/SRR5634862/SRR5634862.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040028-04A.3-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040028-04A.3-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-04A.3	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-04A.3-01D	DNA	EFO	SRS1761151	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-04A.3-01D A59177 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59177	SRX2238858	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040028-04A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040028-04A.3-01D A59177 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59177_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634862	@dbgap@:reads/SRP011999/SRS1761151/SRX2238858/SRR5634862/SRR5634862.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040028-04A.3-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040028-04A.3-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040028.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-14A.1-01D	DNA	EFO	SRS1761140	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-14A.1-01D A59280 library	PAIRED	GENOMIC	WGS	RANDOM	392	A59280	SRX2238848	"WGS analysis of normal sample TARGET-15-SJMPAL040028-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040028-14A.1-01D A59280 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59280_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634878	@dbgap@:reads/SRP011999/SRS1761140/SRX2238848/SRR5634878/SRR5634878.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040028.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-14A.1-01D	DNA	EFO	SRS1761140	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-14A.1-01D A59280 library	PAIRED	GENOMIC	WGS	RANDOM	392	A59280	SRX2238848	"WGS analysis of normal sample TARGET-15-SJMPAL040028-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040028-14A.1-01D A59280 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59280_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634878	@dbgap@:reads/SRP011999/SRS1761140/SRX2238848/SRR5634878/SRR5634878.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040028.quality_tagged.vcf	3						
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-14A.1-01D	DNA	EFO	SRS1761140	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-14A.1-01D A59280 library	PAIRED	GENOMIC	WGS	RANDOM	392	A59280	SRX2238848	"WGS analysis of normal sample TARGET-15-SJMPAL040028-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040028-14A.1-01D A59280 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59280_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634878	@dbgap@:reads/SRP011999/SRS1761140/SRX2238848/SRR5634878/SRR5634878.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040028-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040028-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-14A.1-01D	DNA	EFO	SRS1761140	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-14A.1-01D A59280 library	PAIRED	GENOMIC	WGS	RANDOM	392	A59280	SRX2238848	"WGS analysis of normal sample TARGET-15-SJMPAL040028-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040028-14A.1-01D A59280 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59280_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634878	@dbgap@:reads/SRP011999/SRS1761140/SRX2238848/SRR5634878/SRR5634878.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040028.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-14A.1-01D	DNA	EFO	SRS1761140	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-14A.1-01D A59280 library	PAIRED	GENOMIC	WGS	RANDOM	392	A59280	SRX2238848	"WGS analysis of normal sample TARGET-15-SJMPAL040028-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040028-14A.1-01D A59280 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59280_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634878	@dbgap@:reads/SRP011999/SRS1761140/SRX2238848/SRR5634878/SRR5634878.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040028-04A.1-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040028-04A.1-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-14A.1-01D	DNA	EFO	SRS1761140	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-14A.1-01D A59280 library	PAIRED	GENOMIC	WGS	RANDOM	392	A59280	SRX2238848	"WGS analysis of normal sample TARGET-15-SJMPAL040028-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040028-14A.1-01D A59280 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59280_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634878	@dbgap@:reads/SRP011999/SRS1761140/SRX2238848/SRR5634878/SRR5634878.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040028-04A.1-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040028-04A.1-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040028.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-14A.1-01D	DNA	EFO	SRS1761140	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-14A.1-01D A59280 library	PAIRED	GENOMIC	WGS	RANDOM	392	A59280	SRX2238848	"WGS analysis of normal sample TARGET-15-SJMPAL040028-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040028-14A.1-01D A59280 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59280_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634878	@dbgap@:reads/SRP011999/SRS1761140/SRX2238848/SRR5634878/SRR5634878.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040028-04A.2-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040028-04A.2-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-14A.1-01D	DNA	EFO	SRS1761140	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-14A.1-01D A59280 library	PAIRED	GENOMIC	WGS	RANDOM	392	A59280	SRX2238848	"WGS analysis of normal sample TARGET-15-SJMPAL040028-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040028-14A.1-01D A59280 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59280_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634878	@dbgap@:reads/SRP011999/SRS1761140/SRX2238848/SRR5634878/SRR5634878.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040028-04A.2-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040028-04A.2-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040028.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-14A.1-01D	DNA	EFO	SRS1761140	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-14A.1-01D A59280 library	PAIRED	GENOMIC	WGS	RANDOM	392	A59280	SRX2238848	"WGS analysis of normal sample TARGET-15-SJMPAL040028-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040028-14A.1-01D A59280 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59280_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634878	@dbgap@:reads/SRP011999/SRS1761140/SRX2238848/SRR5634878/SRR5634878.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040028-04A.3-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040028-04A.3-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040028	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040028-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040028-14A.1-01D	DNA	EFO	SRS1761140	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040028-14A.1-01D A59280 library	PAIRED	GENOMIC	WGS	RANDOM	392	A59280	SRX2238848	"WGS analysis of normal sample TARGET-15-SJMPAL040028-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040028-14A.1-01D A59280 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59280_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634878	@dbgap@:reads/SRP011999/SRS1761140/SRX2238848/SRR5634878/SRR5634878.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040028-04A.3-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040028-04A.3-01D_TARGET-15-SJMPAL040028-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040028.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040032	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040032-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040032-09A-01D	DNA	EFO	SRS1761197	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040032-09A-01D A59147 library	PAIRED	GENOMIC	WGS	RANDOM	473	A59147	SRX2238905	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040032-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL040032-09A-01D A59147 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59147_3_lanes_dupsFlagged_reheadered.bam	SRR4415925	@dbgap@:reads/SRP011999/SRS1761197/SRX2238905/SRR4415925/SRR4415925.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040032.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040032	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040032-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040032-09A-01D	DNA	EFO	SRS1761197	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040032-09A-01D A59147 library	PAIRED	GENOMIC	WGS	RANDOM	473	A59147	SRX2238905	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040032-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL040032-09A-01D A59147 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59147_3_lanes_dupsFlagged_reheadered.bam	SRR4415925	@dbgap@:reads/SRP011999/SRS1761197/SRX2238905/SRR4415925/SRR4415925.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040032-09A-01D.fusion.vcf	3						
TARGET-15-SJMPAL040032	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040032-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040032-09A-01D	DNA	EFO	SRS1761197	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040032-09A-01D A59147 library	PAIRED	GENOMIC	WGS	RANDOM	473	A59147	SRX2238905	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040032-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL040032-09A-01D A59147 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59147_3_lanes_dupsFlagged_reheadered.bam	SRR4415925	@dbgap@:reads/SRP011999/SRS1761197/SRX2238905/SRR4415925/SRR4415925.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040032-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL040032	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040032-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040032-09A-01D	DNA	EFO	SRS1761197	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040032-09A-01D A59147 library	PAIRED	GENOMIC	WGS	RANDOM	473	A59147	SRX2238905	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040032-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL040032-09A-01D A59147 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59147_3_lanes_dupsFlagged_reheadered.bam	SRR4415925	@dbgap@:reads/SRP011999/SRS1761197/SRX2238905/SRR4415925/SRR4415925.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040032.quality_tagged.vcf	3						
TARGET-15-SJMPAL040032	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040032-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040032-09A-01D	DNA	EFO	SRS1761197	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040032-09A-01D A59147 library	PAIRED	GENOMIC	WGS	RANDOM	473	A59147	SRX2238905	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040032-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL040032-09A-01D A59147 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59147_3_lanes_dupsFlagged_reheadered.bam	SRR4415925	@dbgap@:reads/SRP011999/SRS1761197/SRX2238905/SRR4415925/SRR4415925.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040032-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040032-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040032	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040032-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040032-09A-01D	DNA	EFO	SRS1761197	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040032-09A-01D A59147 library	PAIRED	GENOMIC	WGS	RANDOM	473	A59147	SRX2238905	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040032-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL040032-09A-01D A59147 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59147_3_lanes_dupsFlagged_reheadered.bam	SRR4415925	@dbgap@:reads/SRP011999/SRS1761197/SRX2238905/SRR4415925/SRR4415925.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040032.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040032	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040032-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040032-09A-01D	DNA	EFO	SRS1761197	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040032-09A-01D A59147 library	PAIRED	GENOMIC	WGS	RANDOM	473	A59147	SRX2238905	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040032-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL040032-09A-01D A59147 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59147_3_lanes_dupsFlagged_reheadered.bam	SRR4415925	@dbgap@:reads/SRP011999/SRS1761197/SRX2238905/SRR4415925/SRR4415925.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040032-09A-01D_TARGET-15-SJMPAL040032-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040032-09A-01D_TARGET-15-SJMPAL040032-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040032	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040032-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040032-09A-01D	DNA	EFO	SRS1761197	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040032-09A-01D A59147 library	PAIRED	GENOMIC	WGS	RANDOM	473	A59147	SRX2238905	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040032-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL040032-09A-01D A59147 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59147_3_lanes_dupsFlagged_reheadered.bam	SRR4415925	@dbgap@:reads/SRP011999/SRS1761197/SRX2238905/SRR4415925/SRR4415925.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040032-09A-01D_TARGET-15-SJMPAL040032-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040032-09A-01D_TARGET-15-SJMPAL040032-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040032.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040032	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040032-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040032-14A.1-01D	DNA	EFO	SRS1761166	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040032-14A.1-01D A59256 library	PAIRED	GENOMIC	WGS	RANDOM	441	A59256	SRX2238874	"WGS analysis of normal sample TARGET-15-SJMPAL040032-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040032-14A.1-01D A59256 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59256_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634859	@dbgap@:reads/SRP011999/SRS1761166/SRX2238874/SRR5634859/SRR5634859.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040032.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040032	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040032-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040032-14A.1-01D	DNA	EFO	SRS1761166	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040032-14A.1-01D A59256 library	PAIRED	GENOMIC	WGS	RANDOM	441	A59256	SRX2238874	"WGS analysis of normal sample TARGET-15-SJMPAL040032-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040032-14A.1-01D A59256 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59256_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634859	@dbgap@:reads/SRP011999/SRS1761166/SRX2238874/SRR5634859/SRR5634859.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040032.quality_tagged.vcf	3						
TARGET-15-SJMPAL040032	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040032-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040032-14A.1-01D	DNA	EFO	SRS1761166	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040032-14A.1-01D A59256 library	PAIRED	GENOMIC	WGS	RANDOM	441	A59256	SRX2238874	"WGS analysis of normal sample TARGET-15-SJMPAL040032-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040032-14A.1-01D A59256 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59256_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634859	@dbgap@:reads/SRP011999/SRS1761166/SRX2238874/SRR5634859/SRR5634859.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040032-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040032-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040032	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040032-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040032-14A.1-01D	DNA	EFO	SRS1761166	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040032-14A.1-01D A59256 library	PAIRED	GENOMIC	WGS	RANDOM	441	A59256	SRX2238874	"WGS analysis of normal sample TARGET-15-SJMPAL040032-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040032-14A.1-01D A59256 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59256_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634859	@dbgap@:reads/SRP011999/SRS1761166/SRX2238874/SRR5634859/SRR5634859.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040032.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040032	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040032-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040032-14A.1-01D	DNA	EFO	SRS1761166	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040032-14A.1-01D A59256 library	PAIRED	GENOMIC	WGS	RANDOM	441	A59256	SRX2238874	"WGS analysis of normal sample TARGET-15-SJMPAL040032-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040032-14A.1-01D A59256 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59256_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634859	@dbgap@:reads/SRP011999/SRS1761166/SRX2238874/SRR5634859/SRR5634859.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040032-09A-01D_TARGET-15-SJMPAL040032-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040032-09A-01D_TARGET-15-SJMPAL040032-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040032	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040032-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040032-14A.1-01D	DNA	EFO	SRS1761166	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040032-14A.1-01D A59256 library	PAIRED	GENOMIC	WGS	RANDOM	441	A59256	SRX2238874	"WGS analysis of normal sample TARGET-15-SJMPAL040032-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040032-14A.1-01D A59256 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59256_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634859	@dbgap@:reads/SRP011999/SRS1761166/SRX2238874/SRR5634859/SRR5634859.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040032-09A-01D_TARGET-15-SJMPAL040032-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040032-09A-01D_TARGET-15-SJMPAL040032-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040032.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.1	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.1-01D	DNA	EFO	SRS1761190	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.1-01D A59180 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59180	SRX2238898	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.1-01D A59180 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59180_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634831	@dbgap@:reads/SRP011999/SRS1761190/SRX2238898/SRR5634831/SRR5634831.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040036.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.1	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.1-01D	DNA	EFO	SRS1761190	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.1-01D A59180 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59180	SRX2238898	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.1-01D A59180 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59180_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634831	@dbgap@:reads/SRP011999/SRS1761190/SRX2238898/SRR5634831/SRR5634831.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040036-03A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040036.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.1	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.1-01D	DNA	EFO	SRS1761190	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.1-01D A59180 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59180	SRX2238898	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.1-01D A59180 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59180_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634831	@dbgap@:reads/SRP011999/SRS1761190/SRX2238898/SRR5634831/SRR5634831.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040036-03A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040036.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.1	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.1-01D	DNA	EFO	SRS1761190	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.1-01D A59180 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59180	SRX2238898	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.1-01D A59180 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59180_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634831	@dbgap@:reads/SRP011999/SRS1761190/SRX2238898/SRR5634831/SRR5634831.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040036-03A.1-01D.indel.vcf	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.1	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.1-01D	DNA	EFO	SRS1761190	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.1-01D A59180 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59180	SRX2238898	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.1-01D A59180 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59180_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634831	@dbgap@:reads/SRP011999/SRS1761190/SRX2238898/SRR5634831/SRR5634831.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040036.quality_tagged.vcf	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.1	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.1-01D	DNA	EFO	SRS1761190	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.1-01D A59180 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59180	SRX2238898	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.1-01D A59180 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59180_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634831	@dbgap@:reads/SRP011999/SRS1761190/SRX2238898/SRR5634831/SRR5634831.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040036-03A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040036-03A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.1	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.1-01D	DNA	EFO	SRS1761190	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.1-01D A59180 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59180	SRX2238898	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.1-01D A59180 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59180_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634831	@dbgap@:reads/SRP011999/SRS1761190/SRX2238898/SRR5634831/SRR5634831.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040036.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.1	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.1-01D	DNA	EFO	SRS1761190	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.1-01D A59180 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59180	SRX2238898	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.1-01D A59180 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59180_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634831	@dbgap@:reads/SRP011999/SRS1761190/SRX2238898/SRR5634831/SRR5634831.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040036-03A.1-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040036-03A.1-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.1	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.1-01D	DNA	EFO	SRS1761190	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.1-01D A59180 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59180	SRX2238898	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.1-01D A59180 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59180_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634831	@dbgap@:reads/SRP011999/SRS1761190/SRX2238898/SRR5634831/SRR5634831.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040036-03A.1-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040036-03A.1-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040036.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.2	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.2-01D	DNA	EFO	SRS1761104	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.2-01D A59181 library	PAIRED	GENOMIC	WGS	RANDOM	481	A59181	SRX2238812	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.2-01D A59181 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59181_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634843	@dbgap@:reads/SRP011999/SRS1761104/SRX2238812/SRR5634843/SRR5634843.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040036.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.2	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.2-01D	DNA	EFO	SRS1761104	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.2-01D A59181 library	PAIRED	GENOMIC	WGS	RANDOM	481	A59181	SRX2238812	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.2-01D A59181 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59181_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634843	@dbgap@:reads/SRP011999/SRS1761104/SRX2238812/SRR5634843/SRR5634843.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040036-03A.2-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040036.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.2	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.2-01D	DNA	EFO	SRS1761104	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.2-01D A59181 library	PAIRED	GENOMIC	WGS	RANDOM	481	A59181	SRX2238812	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.2-01D A59181 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59181_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634843	@dbgap@:reads/SRP011999/SRS1761104/SRX2238812/SRR5634843/SRR5634843.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040036-03A.2-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040036.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.2	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.2-01D	DNA	EFO	SRS1761104	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.2-01D A59181 library	PAIRED	GENOMIC	WGS	RANDOM	481	A59181	SRX2238812	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.2-01D A59181 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59181_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634843	@dbgap@:reads/SRP011999/SRS1761104/SRX2238812/SRR5634843/SRR5634843.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040036-03A.2-01D.indel.vcf	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.2	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.2-01D	DNA	EFO	SRS1761104	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.2-01D A59181 library	PAIRED	GENOMIC	WGS	RANDOM	481	A59181	SRX2238812	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.2-01D A59181 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59181_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634843	@dbgap@:reads/SRP011999/SRS1761104/SRX2238812/SRR5634843/SRR5634843.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040036.quality_tagged.vcf	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.2	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.2-01D	DNA	EFO	SRS1761104	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.2-01D A59181 library	PAIRED	GENOMIC	WGS	RANDOM	481	A59181	SRX2238812	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.2-01D A59181 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59181_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634843	@dbgap@:reads/SRP011999/SRS1761104/SRX2238812/SRR5634843/SRR5634843.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040036-03A.2-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040036-03A.2-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.2	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.2-01D	DNA	EFO	SRS1761104	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.2-01D A59181 library	PAIRED	GENOMIC	WGS	RANDOM	481	A59181	SRX2238812	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.2-01D A59181 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59181_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634843	@dbgap@:reads/SRP011999/SRS1761104/SRX2238812/SRR5634843/SRR5634843.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040036.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.2	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.2-01D	DNA	EFO	SRS1761104	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.2-01D A59181 library	PAIRED	GENOMIC	WGS	RANDOM	481	A59181	SRX2238812	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.2-01D A59181 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59181_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634843	@dbgap@:reads/SRP011999/SRS1761104/SRX2238812/SRR5634843/SRR5634843.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040036-03A.2-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040036-03A.2-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.2	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.2-01D	DNA	EFO	SRS1761104	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.2-01D A59181 library	PAIRED	GENOMIC	WGS	RANDOM	481	A59181	SRX2238812	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.2-01D A59181 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59181_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634843	@dbgap@:reads/SRP011999/SRS1761104/SRX2238812/SRR5634843/SRR5634843.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040036-03A.2-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040036-03A.2-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040036.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.3	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.3-01D	DNA	EFO	SRS1761155	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.3-01D A59182 library	PAIRED	GENOMIC	WGS	RANDOM	495	A59182	SRX2238863	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.3-01D A59182 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59182_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634869	@dbgap@:reads/SRP011999/SRS1761155/SRX2238863/SRR5634869/SRR5634869.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040036.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.3	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.3-01D	DNA	EFO	SRS1761155	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.3-01D A59182 library	PAIRED	GENOMIC	WGS	RANDOM	495	A59182	SRX2238863	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.3-01D A59182 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59182_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634869	@dbgap@:reads/SRP011999/SRS1761155/SRX2238863/SRR5634869/SRR5634869.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040036-03A.3-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040036.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.3	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.3-01D	DNA	EFO	SRS1761155	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.3-01D A59182 library	PAIRED	GENOMIC	WGS	RANDOM	495	A59182	SRX2238863	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.3-01D A59182 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59182_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634869	@dbgap@:reads/SRP011999/SRS1761155/SRX2238863/SRR5634869/SRR5634869.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040036-03A.3-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040036.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.3	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.3-01D	DNA	EFO	SRS1761155	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.3-01D A59182 library	PAIRED	GENOMIC	WGS	RANDOM	495	A59182	SRX2238863	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.3-01D A59182 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59182_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634869	@dbgap@:reads/SRP011999/SRS1761155/SRX2238863/SRR5634869/SRR5634869.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040036-03A.3-01D.indel.vcf	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.3	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.3-01D	DNA	EFO	SRS1761155	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.3-01D A59182 library	PAIRED	GENOMIC	WGS	RANDOM	495	A59182	SRX2238863	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.3-01D A59182 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59182_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634869	@dbgap@:reads/SRP011999/SRS1761155/SRX2238863/SRR5634869/SRR5634869.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040036.quality_tagged.vcf	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.3	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.3-01D	DNA	EFO	SRS1761155	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.3-01D A59182 library	PAIRED	GENOMIC	WGS	RANDOM	495	A59182	SRX2238863	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.3-01D A59182 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59182_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634869	@dbgap@:reads/SRP011999/SRS1761155/SRX2238863/SRR5634869/SRR5634869.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040036-03A.3-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040036-03A.3-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.3	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.3-01D	DNA	EFO	SRS1761155	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.3-01D A59182 library	PAIRED	GENOMIC	WGS	RANDOM	495	A59182	SRX2238863	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.3-01D A59182 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59182_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634869	@dbgap@:reads/SRP011999/SRS1761155/SRX2238863/SRR5634869/SRR5634869.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040036.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.3	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.3-01D	DNA	EFO	SRS1761155	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.3-01D A59182 library	PAIRED	GENOMIC	WGS	RANDOM	495	A59182	SRX2238863	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.3-01D A59182 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59182_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634869	@dbgap@:reads/SRP011999/SRS1761155/SRX2238863/SRR5634869/SRR5634869.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040036-03A.3-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040036-03A.3-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.3	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.3-01D	DNA	EFO	SRS1761155	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.3-01D A59182 library	PAIRED	GENOMIC	WGS	RANDOM	495	A59182	SRX2238863	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.3-01D A59182 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59182_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634869	@dbgap@:reads/SRP011999/SRS1761155/SRX2238863/SRR5634869/SRR5634869.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040036-03A.3-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040036-03A.3-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040036.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.4	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.4-01D	DNA	EFO	SRS1761194	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.4-01D A59183 library	PAIRED	GENOMIC	WGS	RANDOM	497	A59183	SRX2238902	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.4-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.4-01D A59183 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59183_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634839	@dbgap@:reads/SRP011999/SRS1761194/SRX2238902/SRR5634839/SRR5634839.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040036.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.4	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.4-01D	DNA	EFO	SRS1761194	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.4-01D A59183 library	PAIRED	GENOMIC	WGS	RANDOM	497	A59183	SRX2238902	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.4-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.4-01D A59183 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59183_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634839	@dbgap@:reads/SRP011999/SRS1761194/SRX2238902/SRR5634839/SRR5634839.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040036-03A.4-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040036.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.4	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.4-01D	DNA	EFO	SRS1761194	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.4-01D A59183 library	PAIRED	GENOMIC	WGS	RANDOM	497	A59183	SRX2238902	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.4-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.4-01D A59183 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59183_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634839	@dbgap@:reads/SRP011999/SRS1761194/SRX2238902/SRR5634839/SRR5634839.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040036-03A.4-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040036.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.4	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.4-01D	DNA	EFO	SRS1761194	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.4-01D A59183 library	PAIRED	GENOMIC	WGS	RANDOM	497	A59183	SRX2238902	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.4-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.4-01D A59183 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59183_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634839	@dbgap@:reads/SRP011999/SRS1761194/SRX2238902/SRR5634839/SRR5634839.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040036-03A.4-01D.indel.vcf	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.4	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.4-01D	DNA	EFO	SRS1761194	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.4-01D A59183 library	PAIRED	GENOMIC	WGS	RANDOM	497	A59183	SRX2238902	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.4-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.4-01D A59183 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59183_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634839	@dbgap@:reads/SRP011999/SRS1761194/SRX2238902/SRR5634839/SRR5634839.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040036.quality_tagged.vcf	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.4	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.4-01D	DNA	EFO	SRS1761194	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.4-01D A59183 library	PAIRED	GENOMIC	WGS	RANDOM	497	A59183	SRX2238902	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.4-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.4-01D A59183 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59183_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634839	@dbgap@:reads/SRP011999/SRS1761194/SRX2238902/SRR5634839/SRR5634839.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040036-03A.4-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040036-03A.4-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.4	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.4-01D	DNA	EFO	SRS1761194	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.4-01D A59183 library	PAIRED	GENOMIC	WGS	RANDOM	497	A59183	SRX2238902	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.4-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.4-01D A59183 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59183_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634839	@dbgap@:reads/SRP011999/SRS1761194/SRX2238902/SRR5634839/SRR5634839.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040036.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.4	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.4-01D	DNA	EFO	SRS1761194	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.4-01D A59183 library	PAIRED	GENOMIC	WGS	RANDOM	497	A59183	SRX2238902	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.4-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.4-01D A59183 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59183_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634839	@dbgap@:reads/SRP011999/SRS1761194/SRX2238902/SRR5634839/SRR5634839.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040036-03A.4-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040036-03A.4-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-03A.4	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-03A.4-01D	DNA	EFO	SRS1761194	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-03A.4-01D A59183 library	PAIRED	GENOMIC	WGS	RANDOM	497	A59183	SRX2238902	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040036-03A.4-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040036-03A.4-01D A59183 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59183_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634839	@dbgap@:reads/SRP011999/SRS1761194/SRX2238902/SRR5634839/SRR5634839.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040036-03A.4-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040036-03A.4-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040036.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-14A-01D	DNA	EFO	SRS1761189	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-14A-01D A59282 library	PAIRED	GENOMIC	WGS	RANDOM	444	A59282	SRX2238896	"WGS analysis of normal sample TARGET-15-SJMPAL040036-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040036-14A-01D A59282 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59282_2_lanes_dupsFlagged_reheadered.bam	SRR4415915	@dbgap@:reads/SRP011999/SRS1761189/SRX2238896/SRR4415915/SRR4415915.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040036.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-14A-01D	DNA	EFO	SRS1761189	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-14A-01D A59282 library	PAIRED	GENOMIC	WGS	RANDOM	444	A59282	SRX2238896	"WGS analysis of normal sample TARGET-15-SJMPAL040036-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040036-14A-01D A59282 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59282_2_lanes_dupsFlagged_reheadered.bam	SRR4415915	@dbgap@:reads/SRP011999/SRS1761189/SRX2238896/SRR4415915/SRR4415915.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040036.quality_tagged.vcf	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-14A-01D	DNA	EFO	SRS1761189	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-14A-01D A59282 library	PAIRED	GENOMIC	WGS	RANDOM	444	A59282	SRX2238896	"WGS analysis of normal sample TARGET-15-SJMPAL040036-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040036-14A-01D A59282 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59282_2_lanes_dupsFlagged_reheadered.bam	SRR4415915	@dbgap@:reads/SRP011999/SRS1761189/SRX2238896/SRR4415915/SRR4415915.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040036-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040036-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-14A-01D	DNA	EFO	SRS1761189	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-14A-01D A59282 library	PAIRED	GENOMIC	WGS	RANDOM	444	A59282	SRX2238896	"WGS analysis of normal sample TARGET-15-SJMPAL040036-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040036-14A-01D A59282 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59282_2_lanes_dupsFlagged_reheadered.bam	SRR4415915	@dbgap@:reads/SRP011999/SRS1761189/SRX2238896/SRR4415915/SRR4415915.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040036.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-14A-01D	DNA	EFO	SRS1761189	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-14A-01D A59282 library	PAIRED	GENOMIC	WGS	RANDOM	444	A59282	SRX2238896	"WGS analysis of normal sample TARGET-15-SJMPAL040036-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040036-14A-01D A59282 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59282_2_lanes_dupsFlagged_reheadered.bam	SRR4415915	@dbgap@:reads/SRP011999/SRS1761189/SRX2238896/SRR4415915/SRR4415915.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040036-03A.1-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040036-03A.1-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-14A-01D	DNA	EFO	SRS1761189	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-14A-01D A59282 library	PAIRED	GENOMIC	WGS	RANDOM	444	A59282	SRX2238896	"WGS analysis of normal sample TARGET-15-SJMPAL040036-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040036-14A-01D A59282 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59282_2_lanes_dupsFlagged_reheadered.bam	SRR4415915	@dbgap@:reads/SRP011999/SRS1761189/SRX2238896/SRR4415915/SRR4415915.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040036-03A.1-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040036-03A.1-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040036.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-14A-01D	DNA	EFO	SRS1761189	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-14A-01D A59282 library	PAIRED	GENOMIC	WGS	RANDOM	444	A59282	SRX2238896	"WGS analysis of normal sample TARGET-15-SJMPAL040036-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040036-14A-01D A59282 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59282_2_lanes_dupsFlagged_reheadered.bam	SRR4415915	@dbgap@:reads/SRP011999/SRS1761189/SRX2238896/SRR4415915/SRR4415915.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040036-03A.2-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040036-03A.2-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-14A-01D	DNA	EFO	SRS1761189	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-14A-01D A59282 library	PAIRED	GENOMIC	WGS	RANDOM	444	A59282	SRX2238896	"WGS analysis of normal sample TARGET-15-SJMPAL040036-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040036-14A-01D A59282 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59282_2_lanes_dupsFlagged_reheadered.bam	SRR4415915	@dbgap@:reads/SRP011999/SRS1761189/SRX2238896/SRR4415915/SRR4415915.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040036-03A.2-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040036-03A.2-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040036.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-14A-01D	DNA	EFO	SRS1761189	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-14A-01D A59282 library	PAIRED	GENOMIC	WGS	RANDOM	444	A59282	SRX2238896	"WGS analysis of normal sample TARGET-15-SJMPAL040036-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040036-14A-01D A59282 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59282_2_lanes_dupsFlagged_reheadered.bam	SRR4415915	@dbgap@:reads/SRP011999/SRS1761189/SRX2238896/SRR4415915/SRR4415915.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040036-03A.3-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040036-03A.3-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-14A-01D	DNA	EFO	SRS1761189	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-14A-01D A59282 library	PAIRED	GENOMIC	WGS	RANDOM	444	A59282	SRX2238896	"WGS analysis of normal sample TARGET-15-SJMPAL040036-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040036-14A-01D A59282 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59282_2_lanes_dupsFlagged_reheadered.bam	SRR4415915	@dbgap@:reads/SRP011999/SRS1761189/SRX2238896/SRR4415915/SRR4415915.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040036-03A.3-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040036-03A.3-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040036.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-14A-01D	DNA	EFO	SRS1761189	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-14A-01D A59282 library	PAIRED	GENOMIC	WGS	RANDOM	444	A59282	SRX2238896	"WGS analysis of normal sample TARGET-15-SJMPAL040036-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040036-14A-01D A59282 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59282_2_lanes_dupsFlagged_reheadered.bam	SRR4415915	@dbgap@:reads/SRP011999/SRS1761189/SRX2238896/SRR4415915/SRR4415915.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040036-03A.4-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040036-03A.4-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040036	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040036-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040036-14A-01D	DNA	EFO	SRS1761189	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040036-14A-01D A59282 library	PAIRED	GENOMIC	WGS	RANDOM	444	A59282	SRX2238896	"WGS analysis of normal sample TARGET-15-SJMPAL040036-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040036-14A-01D A59282 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59282_2_lanes_dupsFlagged_reheadered.bam	SRR4415915	@dbgap@:reads/SRP011999/SRS1761189/SRX2238896/SRR4415915/SRR4415915.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040036-03A.4-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040036-03A.4-01D_TARGET-15-SJMPAL040036-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040036.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040037	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040037-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040037-09A-01D	DNA	EFO	SRS1761148	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040037-09A-01D A59166 library	PAIRED	GENOMIC	WGS	RANDOM	493	A59166	SRX2238856	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040037-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL040037-09A-01D A59166 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59166_3_lanes_dupsFlagged_reheadered.bam	SRR4415907	@dbgap@:reads/SRP011999/SRS1761148/SRX2238856/SRR4415907/SRR4415907.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040037.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040037	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040037-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040037-09A-01D	DNA	EFO	SRS1761148	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040037-09A-01D A59166 library	PAIRED	GENOMIC	WGS	RANDOM	493	A59166	SRX2238856	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040037-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL040037-09A-01D A59166 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59166_3_lanes_dupsFlagged_reheadered.bam	SRR4415907	@dbgap@:reads/SRP011999/SRS1761148/SRX2238856/SRR4415907/SRR4415907.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040037-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040037.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL040037	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040037-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040037-09A-01D	DNA	EFO	SRS1761148	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040037-09A-01D A59166 library	PAIRED	GENOMIC	WGS	RANDOM	493	A59166	SRX2238856	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040037-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL040037-09A-01D A59166 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59166_3_lanes_dupsFlagged_reheadered.bam	SRR4415907	@dbgap@:reads/SRP011999/SRS1761148/SRX2238856/SRR4415907/SRR4415907.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040037-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040037.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL040037	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040037-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040037-09A-01D	DNA	EFO	SRS1761148	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040037-09A-01D A59166 library	PAIRED	GENOMIC	WGS	RANDOM	493	A59166	SRX2238856	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040037-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL040037-09A-01D A59166 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59166_3_lanes_dupsFlagged_reheadered.bam	SRR4415907	@dbgap@:reads/SRP011999/SRS1761148/SRX2238856/SRR4415907/SRR4415907.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040037-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL040037	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040037-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040037-09A-01D	DNA	EFO	SRS1761148	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040037-09A-01D A59166 library	PAIRED	GENOMIC	WGS	RANDOM	493	A59166	SRX2238856	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040037-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL040037-09A-01D A59166 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59166_3_lanes_dupsFlagged_reheadered.bam	SRR4415907	@dbgap@:reads/SRP011999/SRS1761148/SRX2238856/SRR4415907/SRR4415907.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040037.quality_tagged.vcf	3						
TARGET-15-SJMPAL040037	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040037-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040037-09A-01D	DNA	EFO	SRS1761148	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040037-09A-01D A59166 library	PAIRED	GENOMIC	WGS	RANDOM	493	A59166	SRX2238856	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040037-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL040037-09A-01D A59166 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59166_3_lanes_dupsFlagged_reheadered.bam	SRR4415907	@dbgap@:reads/SRP011999/SRS1761148/SRX2238856/SRR4415907/SRR4415907.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040037-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040037-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040037	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040037-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040037-09A-01D	DNA	EFO	SRS1761148	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040037-09A-01D A59166 library	PAIRED	GENOMIC	WGS	RANDOM	493	A59166	SRX2238856	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040037-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL040037-09A-01D A59166 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59166_3_lanes_dupsFlagged_reheadered.bam	SRR4415907	@dbgap@:reads/SRP011999/SRS1761148/SRX2238856/SRR4415907/SRR4415907.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040037.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040037	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040037-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040037-09A-01D	DNA	EFO	SRS1761148	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040037-09A-01D A59166 library	PAIRED	GENOMIC	WGS	RANDOM	493	A59166	SRX2238856	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040037-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL040037-09A-01D A59166 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59166_3_lanes_dupsFlagged_reheadered.bam	SRR4415907	@dbgap@:reads/SRP011999/SRS1761148/SRX2238856/SRR4415907/SRR4415907.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040037-09A-01D_TARGET-15-SJMPAL040037-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040037-09A-01D_TARGET-15-SJMPAL040037-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040037	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040037-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040037-09A-01D	DNA	EFO	SRS1761148	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040037-09A-01D A59166 library	PAIRED	GENOMIC	WGS	RANDOM	493	A59166	SRX2238856	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040037-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL040037-09A-01D A59166 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59166_3_lanes_dupsFlagged_reheadered.bam	SRR4415907	@dbgap@:reads/SRP011999/SRS1761148/SRX2238856/SRR4415907/SRR4415907.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040037-09A-01D_TARGET-15-SJMPAL040037-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040037-09A-01D_TARGET-15-SJMPAL040037-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040037.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040037	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040037-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040037-14A-01D	DNA	EFO	SRS1761161	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040037-14A-01D A59275 library	PAIRED	GENOMIC	WGS	RANDOM	435	A59275	SRX2238869	"WGS analysis of normal sample TARGET-15-SJMPAL040037-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040037-14A-01D A59275 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59275_2_lanes_dupsFlagged_reheadered.bam	SRR4415833	@dbgap@:reads/SRP011999/SRS1761161/SRX2238869/SRR4415833/SRR4415833.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040037.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040037	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040037-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040037-14A-01D	DNA	EFO	SRS1761161	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040037-14A-01D A59275 library	PAIRED	GENOMIC	WGS	RANDOM	435	A59275	SRX2238869	"WGS analysis of normal sample TARGET-15-SJMPAL040037-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040037-14A-01D A59275 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59275_2_lanes_dupsFlagged_reheadered.bam	SRR4415833	@dbgap@:reads/SRP011999/SRS1761161/SRX2238869/SRR4415833/SRR4415833.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040037.quality_tagged.vcf	3						
TARGET-15-SJMPAL040037	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040037-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040037-14A-01D	DNA	EFO	SRS1761161	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040037-14A-01D A59275 library	PAIRED	GENOMIC	WGS	RANDOM	435	A59275	SRX2238869	"WGS analysis of normal sample TARGET-15-SJMPAL040037-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040037-14A-01D A59275 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59275_2_lanes_dupsFlagged_reheadered.bam	SRR4415833	@dbgap@:reads/SRP011999/SRS1761161/SRX2238869/SRR4415833/SRR4415833.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040037-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040037-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040037	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040037-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040037-14A-01D	DNA	EFO	SRS1761161	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040037-14A-01D A59275 library	PAIRED	GENOMIC	WGS	RANDOM	435	A59275	SRX2238869	"WGS analysis of normal sample TARGET-15-SJMPAL040037-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040037-14A-01D A59275 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59275_2_lanes_dupsFlagged_reheadered.bam	SRR4415833	@dbgap@:reads/SRP011999/SRS1761161/SRX2238869/SRR4415833/SRR4415833.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040037.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040037	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040037-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040037-14A-01D	DNA	EFO	SRS1761161	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040037-14A-01D A59275 library	PAIRED	GENOMIC	WGS	RANDOM	435	A59275	SRX2238869	"WGS analysis of normal sample TARGET-15-SJMPAL040037-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040037-14A-01D A59275 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59275_2_lanes_dupsFlagged_reheadered.bam	SRR4415833	@dbgap@:reads/SRP011999/SRS1761161/SRX2238869/SRR4415833/SRR4415833.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040037-09A-01D_TARGET-15-SJMPAL040037-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040037-09A-01D_TARGET-15-SJMPAL040037-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040037	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040037-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040037-14A-01D	DNA	EFO	SRS1761161	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040037-14A-01D A59275 library	PAIRED	GENOMIC	WGS	RANDOM	435	A59275	SRX2238869	"WGS analysis of normal sample TARGET-15-SJMPAL040037-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040037-14A-01D A59275 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59275_2_lanes_dupsFlagged_reheadered.bam	SRR4415833	@dbgap@:reads/SRP011999/SRS1761161/SRX2238869/SRR4415833/SRR4415833.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040037-09A-01D_TARGET-15-SJMPAL040037-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040037-09A-01D_TARGET-15-SJMPAL040037-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040037.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040038	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040038-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040038-09A.1-01D	DNA	EFO	SRS1761170	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040038-09A.1-01D A59158 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59158	SRX2238878	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040038-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL040038-09A.1-01D A59158 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59158_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634841	@dbgap@:reads/SRP011999/SRS1761170/SRX2238878/SRR5634841/SRR5634841.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040038.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040038	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040038-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040038-09A.1-01D	DNA	EFO	SRS1761170	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040038-09A.1-01D A59158 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59158	SRX2238878	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040038-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL040038-09A.1-01D A59158 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59158_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634841	@dbgap@:reads/SRP011999/SRS1761170/SRX2238878/SRR5634841/SRR5634841.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040038-09A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040038.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL040038	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040038-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040038-09A.1-01D	DNA	EFO	SRS1761170	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040038-09A.1-01D A59158 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59158	SRX2238878	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040038-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL040038-09A.1-01D A59158 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59158_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634841	@dbgap@:reads/SRP011999/SRS1761170/SRX2238878/SRR5634841/SRR5634841.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040038-09A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040038.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL040038	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040038-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040038-09A.1-01D	DNA	EFO	SRS1761170	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040038-09A.1-01D A59158 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59158	SRX2238878	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040038-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL040038-09A.1-01D A59158 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59158_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634841	@dbgap@:reads/SRP011999/SRS1761170/SRX2238878/SRR5634841/SRR5634841.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040038-09A.1-01D.indel.vcf	3						
TARGET-15-SJMPAL040038	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040038-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040038-09A.1-01D	DNA	EFO	SRS1761170	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040038-09A.1-01D A59158 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59158	SRX2238878	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040038-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL040038-09A.1-01D A59158 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59158_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634841	@dbgap@:reads/SRP011999/SRS1761170/SRX2238878/SRR5634841/SRR5634841.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040038.quality_tagged.vcf	3						
TARGET-15-SJMPAL040038	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040038-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040038-09A.1-01D	DNA	EFO	SRS1761170	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040038-09A.1-01D A59158 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59158	SRX2238878	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040038-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL040038-09A.1-01D A59158 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59158_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634841	@dbgap@:reads/SRP011999/SRS1761170/SRX2238878/SRR5634841/SRR5634841.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040038-09A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040038-09A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040038	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040038-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040038-09A.1-01D	DNA	EFO	SRS1761170	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040038-09A.1-01D A59158 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59158	SRX2238878	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040038-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL040038-09A.1-01D A59158 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59158_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634841	@dbgap@:reads/SRP011999/SRS1761170/SRX2238878/SRR5634841/SRR5634841.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040038.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040038	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040038-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040038-09A.1-01D	DNA	EFO	SRS1761170	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040038-09A.1-01D A59158 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59158	SRX2238878	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040038-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL040038-09A.1-01D A59158 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59158_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634841	@dbgap@:reads/SRP011999/SRS1761170/SRX2238878/SRR5634841/SRR5634841.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040038-09A.1-01D_TARGET-15-SJMPAL040038-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040038-09A.1-01D_TARGET-15-SJMPAL040038-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040038	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040038-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040038-09A.1-01D	DNA	EFO	SRS1761170	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040038-09A.1-01D A59158 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59158	SRX2238878	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040038-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL040038-09A.1-01D A59158 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59158_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634841	@dbgap@:reads/SRP011999/SRS1761170/SRX2238878/SRR5634841/SRR5634841.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040038-09A.1-01D_TARGET-15-SJMPAL040038-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040038-09A.1-01D_TARGET-15-SJMPAL040038-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040038.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040038	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040038-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040038-14A-01D	DNA	EFO	SRS1761167	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040038-14A-01D A59267 library	PAIRED	GENOMIC	WGS	RANDOM	423	A59267	SRX2238875	"WGS analysis of normal sample TARGET-15-SJMPAL040038-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040038-14A-01D A59267 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59267_2_lanes_dupsFlagged_reheadered.bam	SRR4415877	@dbgap@:reads/SRP011999/SRS1761167/SRX2238875/SRR4415877/SRR4415877.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040038.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040038	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040038-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040038-14A-01D	DNA	EFO	SRS1761167	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040038-14A-01D A59267 library	PAIRED	GENOMIC	WGS	RANDOM	423	A59267	SRX2238875	"WGS analysis of normal sample TARGET-15-SJMPAL040038-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040038-14A-01D A59267 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59267_2_lanes_dupsFlagged_reheadered.bam	SRR4415877	@dbgap@:reads/SRP011999/SRS1761167/SRX2238875/SRR4415877/SRR4415877.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040038.quality_tagged.vcf	3						
TARGET-15-SJMPAL040038	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040038-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040038-14A-01D	DNA	EFO	SRS1761167	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040038-14A-01D A59267 library	PAIRED	GENOMIC	WGS	RANDOM	423	A59267	SRX2238875	"WGS analysis of normal sample TARGET-15-SJMPAL040038-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040038-14A-01D A59267 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59267_2_lanes_dupsFlagged_reheadered.bam	SRR4415877	@dbgap@:reads/SRP011999/SRS1761167/SRX2238875/SRR4415877/SRR4415877.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040038-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040038-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040038	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040038-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040038-14A-01D	DNA	EFO	SRS1761167	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040038-14A-01D A59267 library	PAIRED	GENOMIC	WGS	RANDOM	423	A59267	SRX2238875	"WGS analysis of normal sample TARGET-15-SJMPAL040038-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040038-14A-01D A59267 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59267_2_lanes_dupsFlagged_reheadered.bam	SRR4415877	@dbgap@:reads/SRP011999/SRS1761167/SRX2238875/SRR4415877/SRR4415877.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040038.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040038	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040038-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040038-14A-01D	DNA	EFO	SRS1761167	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040038-14A-01D A59267 library	PAIRED	GENOMIC	WGS	RANDOM	423	A59267	SRX2238875	"WGS analysis of normal sample TARGET-15-SJMPAL040038-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040038-14A-01D A59267 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59267_2_lanes_dupsFlagged_reheadered.bam	SRR4415877	@dbgap@:reads/SRP011999/SRS1761167/SRX2238875/SRR4415877/SRR4415877.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040038-09A.1-01D_TARGET-15-SJMPAL040038-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040038-09A.1-01D_TARGET-15-SJMPAL040038-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040038	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040038-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040038-14A-01D	DNA	EFO	SRS1761167	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040038-14A-01D A59267 library	PAIRED	GENOMIC	WGS	RANDOM	423	A59267	SRX2238875	"WGS analysis of normal sample TARGET-15-SJMPAL040038-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL040038-14A-01D A59267 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59267_2_lanes_dupsFlagged_reheadered.bam	SRR4415877	@dbgap@:reads/SRP011999/SRS1761167/SRX2238875/SRR4415877/SRR4415877.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040038-09A.1-01D_TARGET-15-SJMPAL040038-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040038-09A.1-01D_TARGET-15-SJMPAL040038-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040038.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-09A.2-01D	DNA	EFO	SRS1761186	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-09A.2-01D A59178 library	PAIRED	GENOMIC	WGS	RANDOM	489	A59178	SRX2238895	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040039-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040039-09A.2-01D A59178 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59178_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634864	@dbgap@:reads/SRP011999/SRS1761186/SRX2238895/SRR5634864/SRR5634864.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040039.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-09A.2-01D	DNA	EFO	SRS1761186	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-09A.2-01D A59178 library	PAIRED	GENOMIC	WGS	RANDOM	489	A59178	SRX2238895	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040039-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040039-09A.2-01D A59178 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59178_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634864	@dbgap@:reads/SRP011999/SRS1761186/SRX2238895/SRR5634864/SRR5634864.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040039-09A.2-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040039.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-09A.2-01D	DNA	EFO	SRS1761186	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-09A.2-01D A59178 library	PAIRED	GENOMIC	WGS	RANDOM	489	A59178	SRX2238895	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040039-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040039-09A.2-01D A59178 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59178_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634864	@dbgap@:reads/SRP011999/SRS1761186/SRX2238895/SRR5634864/SRR5634864.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040039-09A.2-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040039.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-09A.2-01D	DNA	EFO	SRS1761186	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-09A.2-01D A59178 library	PAIRED	GENOMIC	WGS	RANDOM	489	A59178	SRX2238895	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040039-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040039-09A.2-01D A59178 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59178_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634864	@dbgap@:reads/SRP011999/SRS1761186/SRX2238895/SRR5634864/SRR5634864.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040039-09A.2-01D.indel.vcf	3						
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-09A.2-01D	DNA	EFO	SRS1761186	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-09A.2-01D A59178 library	PAIRED	GENOMIC	WGS	RANDOM	489	A59178	SRX2238895	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040039-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040039-09A.2-01D A59178 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59178_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634864	@dbgap@:reads/SRP011999/SRS1761186/SRX2238895/SRR5634864/SRR5634864.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040039.quality_tagged.vcf	3						
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-09A.2-01D	DNA	EFO	SRS1761186	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-09A.2-01D A59178 library	PAIRED	GENOMIC	WGS	RANDOM	489	A59178	SRX2238895	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040039-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040039-09A.2-01D A59178 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59178_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634864	@dbgap@:reads/SRP011999/SRS1761186/SRX2238895/SRR5634864/SRR5634864.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040039-09A.2-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040039-09A.2-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-09A.2-01D	DNA	EFO	SRS1761186	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-09A.2-01D A59178 library	PAIRED	GENOMIC	WGS	RANDOM	489	A59178	SRX2238895	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040039-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040039-09A.2-01D A59178 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59178_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634864	@dbgap@:reads/SRP011999/SRS1761186/SRX2238895/SRR5634864/SRR5634864.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040039.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-09A.2-01D	DNA	EFO	SRS1761186	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-09A.2-01D A59178 library	PAIRED	GENOMIC	WGS	RANDOM	489	A59178	SRX2238895	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040039-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040039-09A.2-01D A59178 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59178_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634864	@dbgap@:reads/SRP011999/SRS1761186/SRX2238895/SRR5634864/SRR5634864.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040039-09A.2-01D_TARGET-15-SJMPAL040039-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040039-09A.2-01D_TARGET-15-SJMPAL040039-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-09A.2-01D	DNA	EFO	SRS1761186	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-09A.2-01D A59178 library	PAIRED	GENOMIC	WGS	RANDOM	489	A59178	SRX2238895	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040039-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040039-09A.2-01D A59178 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59178_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634864	@dbgap@:reads/SRP011999/SRS1761186/SRX2238895/SRR5634864/SRR5634864.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040039-09A.2-01D_TARGET-15-SJMPAL040039-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040039-09A.2-01D_TARGET-15-SJMPAL040039-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040039.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-09A.3-01D	DNA	EFO	SRS1761129	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-09A.3-01D A59179 library	PAIRED	GENOMIC	WGS	RANDOM	485	A59179	SRX2238838	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040039-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040039-09A.3-01D A59179 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59179_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634845	@dbgap@:reads/SRP011999/SRS1761129/SRX2238838/SRR5634845/SRR5634845.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040039.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-09A.3-01D	DNA	EFO	SRS1761129	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-09A.3-01D A59179 library	PAIRED	GENOMIC	WGS	RANDOM	485	A59179	SRX2238838	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040039-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040039-09A.3-01D A59179 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59179_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634845	@dbgap@:reads/SRP011999/SRS1761129/SRX2238838/SRR5634845/SRR5634845.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040039-09A.3-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040039.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-09A.3-01D	DNA	EFO	SRS1761129	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-09A.3-01D A59179 library	PAIRED	GENOMIC	WGS	RANDOM	485	A59179	SRX2238838	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040039-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040039-09A.3-01D A59179 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59179_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634845	@dbgap@:reads/SRP011999/SRS1761129/SRX2238838/SRR5634845/SRR5634845.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040039-09A.3-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL040039.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-09A.3-01D	DNA	EFO	SRS1761129	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-09A.3-01D A59179 library	PAIRED	GENOMIC	WGS	RANDOM	485	A59179	SRX2238838	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040039-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040039-09A.3-01D A59179 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59179_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634845	@dbgap@:reads/SRP011999/SRS1761129/SRX2238838/SRR5634845/SRR5634845.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL040039-09A.3-01D.indel.vcf	3						
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-09A.3-01D	DNA	EFO	SRS1761129	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-09A.3-01D A59179 library	PAIRED	GENOMIC	WGS	RANDOM	485	A59179	SRX2238838	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040039-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040039-09A.3-01D A59179 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59179_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634845	@dbgap@:reads/SRP011999/SRS1761129/SRX2238838/SRR5634845/SRR5634845.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040039.quality_tagged.vcf	3						
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-09A.3-01D	DNA	EFO	SRS1761129	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-09A.3-01D A59179 library	PAIRED	GENOMIC	WGS	RANDOM	485	A59179	SRX2238838	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040039-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040039-09A.3-01D A59179 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59179_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634845	@dbgap@:reads/SRP011999/SRS1761129/SRX2238838/SRR5634845/SRR5634845.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040039-09A.3-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040039-09A.3-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-09A.3-01D	DNA	EFO	SRS1761129	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-09A.3-01D A59179 library	PAIRED	GENOMIC	WGS	RANDOM	485	A59179	SRX2238838	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040039-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040039-09A.3-01D A59179 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59179_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634845	@dbgap@:reads/SRP011999/SRS1761129/SRX2238838/SRR5634845/SRR5634845.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040039.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-09A.3-01D	DNA	EFO	SRS1761129	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-09A.3-01D A59179 library	PAIRED	GENOMIC	WGS	RANDOM	485	A59179	SRX2238838	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040039-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040039-09A.3-01D A59179 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59179_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634845	@dbgap@:reads/SRP011999/SRS1761129/SRX2238838/SRR5634845/SRR5634845.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040039-09A.3-01D_TARGET-15-SJMPAL040039-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040039-09A.3-01D_TARGET-15-SJMPAL040039-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-09A.3-01D	DNA	EFO	SRS1761129	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-09A.3-01D A59179 library	PAIRED	GENOMIC	WGS	RANDOM	485	A59179	SRX2238838	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL040039-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL040039-09A.3-01D A59179 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59179_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634845	@dbgap@:reads/SRP011999/SRS1761129/SRX2238838/SRR5634845/SRR5634845.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040039-09A.3-01D_TARGET-15-SJMPAL040039-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040039-09A.3-01D_TARGET-15-SJMPAL040039-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040039.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-14A-01D	DNA	EFO	SRS1761172	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-14A-01D A59281 library	PAIRED	GENOMIC	WGS	RANDOM	442	A59281	SRX2238880	"WGS analysis of normal sample TARGET-15-SJMPAL040039-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040039-14A-01D A59281 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59281_2_lanes_dupsFlagged_reheadered.bam	SRR4415840	@dbgap@:reads/SRP011999/SRS1761172/SRX2238880/SRR4415840/SRR4415840.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL040039.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-14A-01D	DNA	EFO	SRS1761172	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-14A-01D A59281 library	PAIRED	GENOMIC	WGS	RANDOM	442	A59281	SRX2238880	"WGS analysis of normal sample TARGET-15-SJMPAL040039-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040039-14A-01D A59281 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59281_2_lanes_dupsFlagged_reheadered.bam	SRR4415840	@dbgap@:reads/SRP011999/SRS1761172/SRX2238880/SRR4415840/SRR4415840.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL040039.quality_tagged.vcf	3						
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-14A-01D	DNA	EFO	SRS1761172	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-14A-01D A59281 library	PAIRED	GENOMIC	WGS	RANDOM	442	A59281	SRX2238880	"WGS analysis of normal sample TARGET-15-SJMPAL040039-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040039-14A-01D A59281 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59281_2_lanes_dupsFlagged_reheadered.bam	SRR4415840	@dbgap@:reads/SRP011999/SRS1761172/SRX2238880/SRR4415840/SRR4415840.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL040039-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL040039-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-14A-01D	DNA	EFO	SRS1761172	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-14A-01D A59281 library	PAIRED	GENOMIC	WGS	RANDOM	442	A59281	SRX2238880	"WGS analysis of normal sample TARGET-15-SJMPAL040039-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040039-14A-01D A59281 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59281_2_lanes_dupsFlagged_reheadered.bam	SRR4415840	@dbgap@:reads/SRP011999/SRS1761172/SRX2238880/SRR4415840/SRR4415840.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040039.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-14A-01D	DNA	EFO	SRS1761172	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-14A-01D A59281 library	PAIRED	GENOMIC	WGS	RANDOM	442	A59281	SRX2238880	"WGS analysis of normal sample TARGET-15-SJMPAL040039-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040039-14A-01D A59281 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59281_2_lanes_dupsFlagged_reheadered.bam	SRR4415840	@dbgap@:reads/SRP011999/SRS1761172/SRX2238880/SRR4415840/SRR4415840.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040039-09A.2-01D_TARGET-15-SJMPAL040039-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040039-09A.2-01D_TARGET-15-SJMPAL040039-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-14A-01D	DNA	EFO	SRS1761172	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-14A-01D A59281 library	PAIRED	GENOMIC	WGS	RANDOM	442	A59281	SRX2238880	"WGS analysis of normal sample TARGET-15-SJMPAL040039-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040039-14A-01D A59281 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59281_2_lanes_dupsFlagged_reheadered.bam	SRR4415840	@dbgap@:reads/SRP011999/SRS1761172/SRX2238880/SRR4415840/SRR4415840.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040039-09A.2-01D_TARGET-15-SJMPAL040039-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040039-09A.2-01D_TARGET-15-SJMPAL040039-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040039.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-14A-01D	DNA	EFO	SRS1761172	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-14A-01D A59281 library	PAIRED	GENOMIC	WGS	RANDOM	442	A59281	SRX2238880	"WGS analysis of normal sample TARGET-15-SJMPAL040039-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040039-14A-01D A59281 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59281_2_lanes_dupsFlagged_reheadered.bam	SRR4415840	@dbgap@:reads/SRP011999/SRS1761172/SRX2238880/SRR4415840/SRR4415840.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040039-09A.3-01D_TARGET-15-SJMPAL040039-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL040039-09A.3-01D_TARGET-15-SJMPAL040039-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL040039	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL040039-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL040039-14A-01D	DNA	EFO	SRS1761172	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL040039-14A-01D A59281 library	PAIRED	GENOMIC	WGS	RANDOM	442	A59281	SRX2238880	"WGS analysis of normal sample TARGET-15-SJMPAL040039-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-18	TARGET-15-SJMPAL040039-14A-01D A59281 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59281_2_lanes_dupsFlagged_reheadered.bam	SRR4415840	@dbgap@:reads/SRP011999/SRS1761172/SRX2238880/SRR4415840/SRR4415840.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL040039-09A.3-01D_TARGET-15-SJMPAL040039-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL040039-09A.3-01D_TARGET-15-SJMPAL040039-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL040039.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL041117	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041117-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041117-09A-01D	DNA	EFO	SRS1761180	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041117-09A-01D A59159 library	PAIRED	GENOMIC	WGS	RANDOM	480	A59159	SRX2238888	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041117-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041117-09A-01D A59159 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59159_3_lanes_dupsFlagged_reheadered.bam	SRR4415852	@dbgap@:reads/SRP011999/SRS1761180/SRX2238888/SRR4415852/SRR4415852.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL041117.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL041117	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041117-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041117-09A-01D	DNA	EFO	SRS1761180	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041117-09A-01D A59159 library	PAIRED	GENOMIC	WGS	RANDOM	480	A59159	SRX2238888	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041117-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041117-09A-01D A59159 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59159_3_lanes_dupsFlagged_reheadered.bam	SRR4415852	@dbgap@:reads/SRP011999/SRS1761180/SRX2238888/SRR4415852/SRR4415852.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL041117-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL041117.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL041117	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041117-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041117-09A-01D	DNA	EFO	SRS1761180	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041117-09A-01D A59159 library	PAIRED	GENOMIC	WGS	RANDOM	480	A59159	SRX2238888	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041117-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041117-09A-01D A59159 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59159_3_lanes_dupsFlagged_reheadered.bam	SRR4415852	@dbgap@:reads/SRP011999/SRS1761180/SRX2238888/SRR4415852/SRR4415852.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL041117-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL041117.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL041117	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041117-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041117-09A-01D	DNA	EFO	SRS1761180	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041117-09A-01D A59159 library	PAIRED	GENOMIC	WGS	RANDOM	480	A59159	SRX2238888	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041117-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041117-09A-01D A59159 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59159_3_lanes_dupsFlagged_reheadered.bam	SRR4415852	@dbgap@:reads/SRP011999/SRS1761180/SRX2238888/SRR4415852/SRR4415852.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL041117-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL041117	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041117-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041117-09A-01D	DNA	EFO	SRS1761180	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041117-09A-01D A59159 library	PAIRED	GENOMIC	WGS	RANDOM	480	A59159	SRX2238888	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041117-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041117-09A-01D A59159 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59159_3_lanes_dupsFlagged_reheadered.bam	SRR4415852	@dbgap@:reads/SRP011999/SRS1761180/SRX2238888/SRR4415852/SRR4415852.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL041117.quality_tagged.vcf	3						
TARGET-15-SJMPAL041117	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041117-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041117-09A-01D	DNA	EFO	SRS1761180	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041117-09A-01D A59159 library	PAIRED	GENOMIC	WGS	RANDOM	480	A59159	SRX2238888	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041117-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041117-09A-01D A59159 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59159_3_lanes_dupsFlagged_reheadered.bam	SRR4415852	@dbgap@:reads/SRP011999/SRS1761180/SRX2238888/SRR4415852/SRR4415852.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL041117-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL041117-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL041117	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041117-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041117-09A-01D	DNA	EFO	SRS1761180	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041117-09A-01D A59159 library	PAIRED	GENOMIC	WGS	RANDOM	480	A59159	SRX2238888	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041117-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041117-09A-01D A59159 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59159_3_lanes_dupsFlagged_reheadered.bam	SRR4415852	@dbgap@:reads/SRP011999/SRS1761180/SRX2238888/SRR4415852/SRR4415852.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL041117.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL041117	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041117-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041117-09A-01D	DNA	EFO	SRS1761180	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041117-09A-01D A59159 library	PAIRED	GENOMIC	WGS	RANDOM	480	A59159	SRX2238888	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041117-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041117-09A-01D A59159 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59159_3_lanes_dupsFlagged_reheadered.bam	SRR4415852	@dbgap@:reads/SRP011999/SRS1761180/SRX2238888/SRR4415852/SRR4415852.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL041117-09A-01D_TARGET-15-SJMPAL041117-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL041117-09A-01D_TARGET-15-SJMPAL041117-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL041117	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041117-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041117-09A-01D	DNA	EFO	SRS1761180	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041117-09A-01D A59159 library	PAIRED	GENOMIC	WGS	RANDOM	480	A59159	SRX2238888	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041117-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041117-09A-01D A59159 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59159_3_lanes_dupsFlagged_reheadered.bam	SRR4415852	@dbgap@:reads/SRP011999/SRS1761180/SRX2238888/SRR4415852/SRR4415852.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL041117-09A-01D_TARGET-15-SJMPAL041117-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL041117-09A-01D_TARGET-15-SJMPAL041117-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL041117.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL041117	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041117-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041117-14A-01D	DNA	EFO	SRS1761205	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041117-14A-01D A59268 library	PAIRED	GENOMIC	WGS	RANDOM	448	A59268	SRX2238914	"WGS analysis of normal sample TARGET-15-SJMPAL041117-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL041117-14A-01D A59268 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59268_2_lanes_dupsFlagged_reheadered.bam	SRR4415905	@dbgap@:reads/SRP011999/SRS1761205/SRX2238914/SRR4415905/SRR4415905.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL041117.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL041117	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041117-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041117-14A-01D	DNA	EFO	SRS1761205	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041117-14A-01D A59268 library	PAIRED	GENOMIC	WGS	RANDOM	448	A59268	SRX2238914	"WGS analysis of normal sample TARGET-15-SJMPAL041117-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL041117-14A-01D A59268 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59268_2_lanes_dupsFlagged_reheadered.bam	SRR4415905	@dbgap@:reads/SRP011999/SRS1761205/SRX2238914/SRR4415905/SRR4415905.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL041117.quality_tagged.vcf	3						
TARGET-15-SJMPAL041117	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041117-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041117-14A-01D	DNA	EFO	SRS1761205	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041117-14A-01D A59268 library	PAIRED	GENOMIC	WGS	RANDOM	448	A59268	SRX2238914	"WGS analysis of normal sample TARGET-15-SJMPAL041117-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL041117-14A-01D A59268 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59268_2_lanes_dupsFlagged_reheadered.bam	SRR4415905	@dbgap@:reads/SRP011999/SRS1761205/SRX2238914/SRR4415905/SRR4415905.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL041117-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL041117-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL041117	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041117-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041117-14A-01D	DNA	EFO	SRS1761205	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041117-14A-01D A59268 library	PAIRED	GENOMIC	WGS	RANDOM	448	A59268	SRX2238914	"WGS analysis of normal sample TARGET-15-SJMPAL041117-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL041117-14A-01D A59268 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59268_2_lanes_dupsFlagged_reheadered.bam	SRR4415905	@dbgap@:reads/SRP011999/SRS1761205/SRX2238914/SRR4415905/SRR4415905.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL041117.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL041117	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041117-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041117-14A-01D	DNA	EFO	SRS1761205	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041117-14A-01D A59268 library	PAIRED	GENOMIC	WGS	RANDOM	448	A59268	SRX2238914	"WGS analysis of normal sample TARGET-15-SJMPAL041117-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL041117-14A-01D A59268 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59268_2_lanes_dupsFlagged_reheadered.bam	SRR4415905	@dbgap@:reads/SRP011999/SRS1761205/SRX2238914/SRR4415905/SRR4415905.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL041117-09A-01D_TARGET-15-SJMPAL041117-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL041117-09A-01D_TARGET-15-SJMPAL041117-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL041117	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041117-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041117-14A-01D	DNA	EFO	SRS1761205	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041117-14A-01D A59268 library	PAIRED	GENOMIC	WGS	RANDOM	448	A59268	SRX2238914	"WGS analysis of normal sample TARGET-15-SJMPAL041117-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL041117-14A-01D A59268 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59268_2_lanes_dupsFlagged_reheadered.bam	SRR4415905	@dbgap@:reads/SRP011999/SRS1761205/SRX2238914/SRR4415905/SRR4415905.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL041117-09A-01D_TARGET-15-SJMPAL041117-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL041117-09A-01D_TARGET-15-SJMPAL041117-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL041117.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL041119	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041119-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041119-09A-01D	DNA	EFO	SRS1761203	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041119-09A-01D A59160 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59160	SRX2238911	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041119-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041119-09A-01D A59160 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59160_3_lanes_dupsFlagged_reheadered.bam	SRR4415882	@dbgap@:reads/SRP011999/SRS1761203/SRX2238911/SRR4415882/SRR4415882.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL041119.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL041119	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041119-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041119-09A-01D	DNA	EFO	SRS1761203	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041119-09A-01D A59160 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59160	SRX2238911	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041119-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041119-09A-01D A59160 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59160_3_lanes_dupsFlagged_reheadered.bam	SRR4415882	@dbgap@:reads/SRP011999/SRS1761203/SRX2238911/SRR4415882/SRR4415882.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL041119-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL041119.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL041119	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041119-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041119-09A-01D	DNA	EFO	SRS1761203	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041119-09A-01D A59160 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59160	SRX2238911	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041119-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041119-09A-01D A59160 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59160_3_lanes_dupsFlagged_reheadered.bam	SRR4415882	@dbgap@:reads/SRP011999/SRS1761203/SRX2238911/SRR4415882/SRR4415882.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL041119-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL041119.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL041119	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041119-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041119-09A-01D	DNA	EFO	SRS1761203	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041119-09A-01D A59160 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59160	SRX2238911	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041119-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041119-09A-01D A59160 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59160_3_lanes_dupsFlagged_reheadered.bam	SRR4415882	@dbgap@:reads/SRP011999/SRS1761203/SRX2238911/SRR4415882/SRR4415882.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL041119-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL041119	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041119-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041119-09A-01D	DNA	EFO	SRS1761203	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041119-09A-01D A59160 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59160	SRX2238911	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041119-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041119-09A-01D A59160 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59160_3_lanes_dupsFlagged_reheadered.bam	SRR4415882	@dbgap@:reads/SRP011999/SRS1761203/SRX2238911/SRR4415882/SRR4415882.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL041119.quality_tagged.vcf	3						
TARGET-15-SJMPAL041119	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041119-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041119-09A-01D	DNA	EFO	SRS1761203	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041119-09A-01D A59160 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59160	SRX2238911	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041119-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041119-09A-01D A59160 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59160_3_lanes_dupsFlagged_reheadered.bam	SRR4415882	@dbgap@:reads/SRP011999/SRS1761203/SRX2238911/SRR4415882/SRR4415882.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL041119-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL041119-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL041119	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041119-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041119-09A-01D	DNA	EFO	SRS1761203	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041119-09A-01D A59160 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59160	SRX2238911	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041119-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041119-09A-01D A59160 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59160_3_lanes_dupsFlagged_reheadered.bam	SRR4415882	@dbgap@:reads/SRP011999/SRS1761203/SRX2238911/SRR4415882/SRR4415882.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL041119.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL041119	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041119-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041119-09A-01D	DNA	EFO	SRS1761203	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041119-09A-01D A59160 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59160	SRX2238911	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041119-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041119-09A-01D A59160 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59160_3_lanes_dupsFlagged_reheadered.bam	SRR4415882	@dbgap@:reads/SRP011999/SRS1761203/SRX2238911/SRR4415882/SRR4415882.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL041119-09A-01D_TARGET-15-SJMPAL041119-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL041119-09A-01D_TARGET-15-SJMPAL041119-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL041119	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041119-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041119-09A-01D	DNA	EFO	SRS1761203	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041119-09A-01D A59160 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59160	SRX2238911	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041119-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041119-09A-01D A59160 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59160_3_lanes_dupsFlagged_reheadered.bam	SRR4415882	@dbgap@:reads/SRP011999/SRS1761203/SRX2238911/SRR4415882/SRR4415882.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL041119-09A-01D_TARGET-15-SJMPAL041119-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL041119-09A-01D_TARGET-15-SJMPAL041119-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL041119.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL041119	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041119-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041119-14A-01D	DNA	EFO	SRS1761114	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041119-14A-01D A59269 library	PAIRED	GENOMIC	WGS	RANDOM	446	A59269	SRX2238822	"WGS analysis of normal sample TARGET-15-SJMPAL041119-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL041119-14A-01D A59269 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59269_2_lanes_dupsFlagged_reheadered.bam	SRR4415917	@dbgap@:reads/SRP011999/SRS1761114/SRX2238822/SRR4415917/SRR4415917.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL041119.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL041119	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041119-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041119-14A-01D	DNA	EFO	SRS1761114	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041119-14A-01D A59269 library	PAIRED	GENOMIC	WGS	RANDOM	446	A59269	SRX2238822	"WGS analysis of normal sample TARGET-15-SJMPAL041119-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL041119-14A-01D A59269 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59269_2_lanes_dupsFlagged_reheadered.bam	SRR4415917	@dbgap@:reads/SRP011999/SRS1761114/SRX2238822/SRR4415917/SRR4415917.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL041119.quality_tagged.vcf	3						
TARGET-15-SJMPAL041119	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041119-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041119-14A-01D	DNA	EFO	SRS1761114	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041119-14A-01D A59269 library	PAIRED	GENOMIC	WGS	RANDOM	446	A59269	SRX2238822	"WGS analysis of normal sample TARGET-15-SJMPAL041119-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL041119-14A-01D A59269 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59269_2_lanes_dupsFlagged_reheadered.bam	SRR4415917	@dbgap@:reads/SRP011999/SRS1761114/SRX2238822/SRR4415917/SRR4415917.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL041119-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL041119-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL041119	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041119-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041119-14A-01D	DNA	EFO	SRS1761114	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041119-14A-01D A59269 library	PAIRED	GENOMIC	WGS	RANDOM	446	A59269	SRX2238822	"WGS analysis of normal sample TARGET-15-SJMPAL041119-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL041119-14A-01D A59269 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59269_2_lanes_dupsFlagged_reheadered.bam	SRR4415917	@dbgap@:reads/SRP011999/SRS1761114/SRX2238822/SRR4415917/SRR4415917.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL041119.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL041119	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041119-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041119-14A-01D	DNA	EFO	SRS1761114	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041119-14A-01D A59269 library	PAIRED	GENOMIC	WGS	RANDOM	446	A59269	SRX2238822	"WGS analysis of normal sample TARGET-15-SJMPAL041119-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL041119-14A-01D A59269 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59269_2_lanes_dupsFlagged_reheadered.bam	SRR4415917	@dbgap@:reads/SRP011999/SRS1761114/SRX2238822/SRR4415917/SRR4415917.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL041119-09A-01D_TARGET-15-SJMPAL041119-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL041119-09A-01D_TARGET-15-SJMPAL041119-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL041119	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041119-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041119-14A-01D	DNA	EFO	SRS1761114	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041119-14A-01D A59269 library	PAIRED	GENOMIC	WGS	RANDOM	446	A59269	SRX2238822	"WGS analysis of normal sample TARGET-15-SJMPAL041119-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL041119-14A-01D A59269 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59269_2_lanes_dupsFlagged_reheadered.bam	SRR4415917	@dbgap@:reads/SRP011999/SRS1761114/SRX2238822/SRR4415917/SRR4415917.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL041119-09A-01D_TARGET-15-SJMPAL041119-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL041119-09A-01D_TARGET-15-SJMPAL041119-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL041119.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL041120	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041120-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041120-09A-01D	DNA	EFO	SRS1761131	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041120-09A-01D A59161 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59161	SRX2238839	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041120-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041120-09A-01D A59161 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59161_3_lanes_dupsFlagged_reheadered.bam	SRR4415888	@dbgap@:reads/SRP011999/SRS1761131/SRX2238839/SRR4415888/SRR4415888.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL041120.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL041120	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041120-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041120-09A-01D	DNA	EFO	SRS1761131	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041120-09A-01D A59161 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59161	SRX2238839	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041120-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041120-09A-01D A59161 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59161_3_lanes_dupsFlagged_reheadered.bam	SRR4415888	@dbgap@:reads/SRP011999/SRS1761131/SRX2238839/SRR4415888/SRR4415888.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL041120-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL041120.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL041120	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041120-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041120-09A-01D	DNA	EFO	SRS1761131	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041120-09A-01D A59161 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59161	SRX2238839	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041120-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041120-09A-01D A59161 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59161_3_lanes_dupsFlagged_reheadered.bam	SRR4415888	@dbgap@:reads/SRP011999/SRS1761131/SRX2238839/SRR4415888/SRR4415888.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL041120-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL041120.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL041120	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041120-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041120-09A-01D	DNA	EFO	SRS1761131	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041120-09A-01D A59161 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59161	SRX2238839	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041120-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041120-09A-01D A59161 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59161_3_lanes_dupsFlagged_reheadered.bam	SRR4415888	@dbgap@:reads/SRP011999/SRS1761131/SRX2238839/SRR4415888/SRR4415888.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL041120-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL041120	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041120-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041120-09A-01D	DNA	EFO	SRS1761131	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041120-09A-01D A59161 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59161	SRX2238839	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041120-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041120-09A-01D A59161 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59161_3_lanes_dupsFlagged_reheadered.bam	SRR4415888	@dbgap@:reads/SRP011999/SRS1761131/SRX2238839/SRR4415888/SRR4415888.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL041120.quality_tagged.vcf	3						
TARGET-15-SJMPAL041120	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041120-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041120-09A-01D	DNA	EFO	SRS1761131	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041120-09A-01D A59161 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59161	SRX2238839	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041120-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041120-09A-01D A59161 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59161_3_lanes_dupsFlagged_reheadered.bam	SRR4415888	@dbgap@:reads/SRP011999/SRS1761131/SRX2238839/SRR4415888/SRR4415888.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL041120-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL041120-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL041120	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041120-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041120-09A-01D	DNA	EFO	SRS1761131	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041120-09A-01D A59161 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59161	SRX2238839	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041120-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041120-09A-01D A59161 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59161_3_lanes_dupsFlagged_reheadered.bam	SRR4415888	@dbgap@:reads/SRP011999/SRS1761131/SRX2238839/SRR4415888/SRR4415888.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL041120.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL041120	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041120-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041120-09A-01D	DNA	EFO	SRS1761131	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041120-09A-01D A59161 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59161	SRX2238839	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041120-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041120-09A-01D A59161 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59161_3_lanes_dupsFlagged_reheadered.bam	SRR4415888	@dbgap@:reads/SRP011999/SRS1761131/SRX2238839/SRR4415888/SRR4415888.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL041120-09A-01D_TARGET-15-SJMPAL041120-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL041120-09A-01D_TARGET-15-SJMPAL041120-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL041120	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041120-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041120-09A-01D	DNA	EFO	SRS1761131	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041120-09A-01D A59161 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59161	SRX2238839	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL041120-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL041120-09A-01D A59161 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59161_3_lanes_dupsFlagged_reheadered.bam	SRR4415888	@dbgap@:reads/SRP011999/SRS1761131/SRX2238839/SRR4415888/SRR4415888.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL041120-09A-01D_TARGET-15-SJMPAL041120-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL041120-09A-01D_TARGET-15-SJMPAL041120-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL041120.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL041120	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041120-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041120-14A-01D	DNA	EFO	SRS1761178	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041120-14A-01D A59270 library	PAIRED	GENOMIC	WGS	RANDOM	452	A59270	SRX2238886	"WGS analysis of normal sample TARGET-15-SJMPAL041120-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL041120-14A-01D A59270 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59270_2_lanes_dupsFlagged_reheadered.bam	SRR4415899	@dbgap@:reads/SRP011999/SRS1761178/SRX2238886/SRR4415899/SRR4415899.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL041120.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL041120	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041120-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041120-14A-01D	DNA	EFO	SRS1761178	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041120-14A-01D A59270 library	PAIRED	GENOMIC	WGS	RANDOM	452	A59270	SRX2238886	"WGS analysis of normal sample TARGET-15-SJMPAL041120-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL041120-14A-01D A59270 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59270_2_lanes_dupsFlagged_reheadered.bam	SRR4415899	@dbgap@:reads/SRP011999/SRS1761178/SRX2238886/SRR4415899/SRR4415899.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL041120.quality_tagged.vcf	3						
TARGET-15-SJMPAL041120	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041120-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041120-14A-01D	DNA	EFO	SRS1761178	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041120-14A-01D A59270 library	PAIRED	GENOMIC	WGS	RANDOM	452	A59270	SRX2238886	"WGS analysis of normal sample TARGET-15-SJMPAL041120-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL041120-14A-01D A59270 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59270_2_lanes_dupsFlagged_reheadered.bam	SRR4415899	@dbgap@:reads/SRP011999/SRS1761178/SRX2238886/SRR4415899/SRR4415899.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL041120-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL041120-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL041120	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041120-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041120-14A-01D	DNA	EFO	SRS1761178	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041120-14A-01D A59270 library	PAIRED	GENOMIC	WGS	RANDOM	452	A59270	SRX2238886	"WGS analysis of normal sample TARGET-15-SJMPAL041120-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL041120-14A-01D A59270 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59270_2_lanes_dupsFlagged_reheadered.bam	SRR4415899	@dbgap@:reads/SRP011999/SRS1761178/SRX2238886/SRR4415899/SRR4415899.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL041120.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL041120	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041120-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041120-14A-01D	DNA	EFO	SRS1761178	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041120-14A-01D A59270 library	PAIRED	GENOMIC	WGS	RANDOM	452	A59270	SRX2238886	"WGS analysis of normal sample TARGET-15-SJMPAL041120-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL041120-14A-01D A59270 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59270_2_lanes_dupsFlagged_reheadered.bam	SRR4415899	@dbgap@:reads/SRP011999/SRS1761178/SRX2238886/SRR4415899/SRR4415899.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL041120-09A-01D_TARGET-15-SJMPAL041120-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL041120-09A-01D_TARGET-15-SJMPAL041120-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL041120	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL041120-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL041120-14A-01D	DNA	EFO	SRS1761178	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL041120-14A-01D A59270 library	PAIRED	GENOMIC	WGS	RANDOM	452	A59270	SRX2238886	"WGS analysis of normal sample TARGET-15-SJMPAL041120-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL041120-14A-01D A59270 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59270_2_lanes_dupsFlagged_reheadered.bam	SRR4415899	@dbgap@:reads/SRP011999/SRS1761178/SRX2238886/SRR4415899/SRR4415899.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL041120-09A-01D_TARGET-15-SJMPAL041120-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL041120-09A-01D_TARGET-15-SJMPAL041120-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL041120.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL042787	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042787-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042787-09A-01D	DNA	EFO	SRS1761164	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042787-09A-01D A59162 library	PAIRED	GENOMIC	WGS	RANDOM	488	A59162	SRX2238872	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042787-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042787-09A-01D A59162 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59162_3_lanes_dupsFlagged_reheadered.bam	SRR4415864	@dbgap@:reads/SRP011999/SRS1761164/SRX2238872/SRR4415864/SRR4415864.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL042787.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042787	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042787-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042787-09A-01D	DNA	EFO	SRS1761164	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042787-09A-01D A59162 library	PAIRED	GENOMIC	WGS	RANDOM	488	A59162	SRX2238872	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042787-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042787-09A-01D A59162 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59162_3_lanes_dupsFlagged_reheadered.bam	SRR4415864	@dbgap@:reads/SRP011999/SRS1761164/SRX2238872/SRR4415864/SRR4415864.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042787-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL042787.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL042787	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042787-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042787-09A-01D	DNA	EFO	SRS1761164	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042787-09A-01D A59162 library	PAIRED	GENOMIC	WGS	RANDOM	488	A59162	SRX2238872	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042787-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042787-09A-01D A59162 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59162_3_lanes_dupsFlagged_reheadered.bam	SRR4415864	@dbgap@:reads/SRP011999/SRS1761164/SRX2238872/SRR4415864/SRR4415864.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042787-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL042787.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL042787	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042787-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042787-09A-01D	DNA	EFO	SRS1761164	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042787-09A-01D A59162 library	PAIRED	GENOMIC	WGS	RANDOM	488	A59162	SRX2238872	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042787-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042787-09A-01D A59162 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59162_3_lanes_dupsFlagged_reheadered.bam	SRR4415864	@dbgap@:reads/SRP011999/SRS1761164/SRX2238872/SRR4415864/SRR4415864.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042787-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL042787	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042787-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042787-09A-01D	DNA	EFO	SRS1761164	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042787-09A-01D A59162 library	PAIRED	GENOMIC	WGS	RANDOM	488	A59162	SRX2238872	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042787-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042787-09A-01D A59162 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59162_3_lanes_dupsFlagged_reheadered.bam	SRR4415864	@dbgap@:reads/SRP011999/SRS1761164/SRX2238872/SRR4415864/SRR4415864.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL042787.quality_tagged.vcf	3						
TARGET-15-SJMPAL042787	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042787-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042787-09A-01D	DNA	EFO	SRS1761164	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042787-09A-01D A59162 library	PAIRED	GENOMIC	WGS	RANDOM	488	A59162	SRX2238872	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042787-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042787-09A-01D A59162 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59162_3_lanes_dupsFlagged_reheadered.bam	SRR4415864	@dbgap@:reads/SRP011999/SRS1761164/SRX2238872/SRR4415864/SRR4415864.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL042787-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL042787-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042787	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042787-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042787-09A-01D	DNA	EFO	SRS1761164	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042787-09A-01D A59162 library	PAIRED	GENOMIC	WGS	RANDOM	488	A59162	SRX2238872	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042787-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042787-09A-01D A59162 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59162_3_lanes_dupsFlagged_reheadered.bam	SRR4415864	@dbgap@:reads/SRP011999/SRS1761164/SRX2238872/SRR4415864/SRR4415864.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042787.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042787	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042787-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042787-09A-01D	DNA	EFO	SRS1761164	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042787-09A-01D A59162 library	PAIRED	GENOMIC	WGS	RANDOM	488	A59162	SRX2238872	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042787-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042787-09A-01D A59162 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59162_3_lanes_dupsFlagged_reheadered.bam	SRR4415864	@dbgap@:reads/SRP011999/SRS1761164/SRX2238872/SRR4415864/SRR4415864.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042787-09A-01D_TARGET-15-SJMPAL042787-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL042787-09A-01D_TARGET-15-SJMPAL042787-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042787	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042787-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042787-09A-01D	DNA	EFO	SRS1761164	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042787-09A-01D A59162 library	PAIRED	GENOMIC	WGS	RANDOM	488	A59162	SRX2238872	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042787-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042787-09A-01D A59162 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59162_3_lanes_dupsFlagged_reheadered.bam	SRR4415864	@dbgap@:reads/SRP011999/SRS1761164/SRX2238872/SRR4415864/SRR4415864.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042787-09A-01D_TARGET-15-SJMPAL042787-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL042787-09A-01D_TARGET-15-SJMPAL042787-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042787.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL042787	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042787-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042787-14A.1-01D	DNA	EFO	SRS1761115	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042787-14A.1-01D A59271 library	PAIRED	GENOMIC	WGS	RANDOM	441	A59271	SRX2238823	"WGS analysis of normal sample TARGET-15-SJMPAL042787-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL042787-14A.1-01D A59271 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59271_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634848	@dbgap@:reads/SRP011999/SRS1761115/SRX2238823/SRR5634848/SRR5634848.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL042787.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042787	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042787-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042787-14A.1-01D	DNA	EFO	SRS1761115	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042787-14A.1-01D A59271 library	PAIRED	GENOMIC	WGS	RANDOM	441	A59271	SRX2238823	"WGS analysis of normal sample TARGET-15-SJMPAL042787-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL042787-14A.1-01D A59271 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59271_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634848	@dbgap@:reads/SRP011999/SRS1761115/SRX2238823/SRR5634848/SRR5634848.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL042787.quality_tagged.vcf	3						
TARGET-15-SJMPAL042787	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042787-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042787-14A.1-01D	DNA	EFO	SRS1761115	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042787-14A.1-01D A59271 library	PAIRED	GENOMIC	WGS	RANDOM	441	A59271	SRX2238823	"WGS analysis of normal sample TARGET-15-SJMPAL042787-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL042787-14A.1-01D A59271 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59271_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634848	@dbgap@:reads/SRP011999/SRS1761115/SRX2238823/SRR5634848/SRR5634848.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL042787-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL042787-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042787	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042787-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042787-14A.1-01D	DNA	EFO	SRS1761115	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042787-14A.1-01D A59271 library	PAIRED	GENOMIC	WGS	RANDOM	441	A59271	SRX2238823	"WGS analysis of normal sample TARGET-15-SJMPAL042787-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL042787-14A.1-01D A59271 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59271_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634848	@dbgap@:reads/SRP011999/SRS1761115/SRX2238823/SRR5634848/SRR5634848.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042787.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042787	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042787-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042787-14A.1-01D	DNA	EFO	SRS1761115	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042787-14A.1-01D A59271 library	PAIRED	GENOMIC	WGS	RANDOM	441	A59271	SRX2238823	"WGS analysis of normal sample TARGET-15-SJMPAL042787-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL042787-14A.1-01D A59271 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59271_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634848	@dbgap@:reads/SRP011999/SRS1761115/SRX2238823/SRR5634848/SRR5634848.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042787-09A-01D_TARGET-15-SJMPAL042787-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL042787-09A-01D_TARGET-15-SJMPAL042787-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042787	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042787-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042787-14A.1-01D	DNA	EFO	SRS1761115	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042787-14A.1-01D A59271 library	PAIRED	GENOMIC	WGS	RANDOM	441	A59271	SRX2238823	"WGS analysis of normal sample TARGET-15-SJMPAL042787-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL042787-14A.1-01D A59271 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59271_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634848	@dbgap@:reads/SRP011999/SRS1761115/SRX2238823/SRR5634848/SRR5634848.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042787-09A-01D_TARGET-15-SJMPAL042787-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL042787-09A-01D_TARGET-15-SJMPAL042787-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042787.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL042791	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042791-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042791-09A-01D	DNA	EFO	SRS1761116	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042791-09A-01D A59167 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59167	SRX2238824	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042791-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042791-09A-01D A59167 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59167_3_lanes_dupsFlagged_reheadered.bam	SRR4415894	@dbgap@:reads/SRP011999/SRS1761116/SRX2238824/SRR4415894/SRR4415894.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL042791.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042791	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042791-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042791-09A-01D	DNA	EFO	SRS1761116	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042791-09A-01D A59167 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59167	SRX2238824	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042791-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042791-09A-01D A59167 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59167_3_lanes_dupsFlagged_reheadered.bam	SRR4415894	@dbgap@:reads/SRP011999/SRS1761116/SRX2238824/SRR4415894/SRR4415894.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042791-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL042791.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL042791	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042791-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042791-09A-01D	DNA	EFO	SRS1761116	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042791-09A-01D A59167 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59167	SRX2238824	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042791-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042791-09A-01D A59167 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59167_3_lanes_dupsFlagged_reheadered.bam	SRR4415894	@dbgap@:reads/SRP011999/SRS1761116/SRX2238824/SRR4415894/SRR4415894.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042791-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL042791.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL042791	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042791-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042791-09A-01D	DNA	EFO	SRS1761116	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042791-09A-01D A59167 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59167	SRX2238824	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042791-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042791-09A-01D A59167 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59167_3_lanes_dupsFlagged_reheadered.bam	SRR4415894	@dbgap@:reads/SRP011999/SRS1761116/SRX2238824/SRR4415894/SRR4415894.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042791-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL042791	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042791-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042791-09A-01D	DNA	EFO	SRS1761116	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042791-09A-01D A59167 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59167	SRX2238824	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042791-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042791-09A-01D A59167 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59167_3_lanes_dupsFlagged_reheadered.bam	SRR4415894	@dbgap@:reads/SRP011999/SRS1761116/SRX2238824/SRR4415894/SRR4415894.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL042791.quality_tagged.vcf	3						
TARGET-15-SJMPAL042791	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042791-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042791-09A-01D	DNA	EFO	SRS1761116	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042791-09A-01D A59167 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59167	SRX2238824	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042791-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042791-09A-01D A59167 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59167_3_lanes_dupsFlagged_reheadered.bam	SRR4415894	@dbgap@:reads/SRP011999/SRS1761116/SRX2238824/SRR4415894/SRR4415894.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL042791-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL042791-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042791	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042791-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042791-09A-01D	DNA	EFO	SRS1761116	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042791-09A-01D A59167 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59167	SRX2238824	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042791-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042791-09A-01D A59167 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59167_3_lanes_dupsFlagged_reheadered.bam	SRR4415894	@dbgap@:reads/SRP011999/SRS1761116/SRX2238824/SRR4415894/SRR4415894.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042791.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042791	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042791-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042791-09A-01D	DNA	EFO	SRS1761116	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042791-09A-01D A59167 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59167	SRX2238824	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042791-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042791-09A-01D A59167 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59167_3_lanes_dupsFlagged_reheadered.bam	SRR4415894	@dbgap@:reads/SRP011999/SRS1761116/SRX2238824/SRR4415894/SRR4415894.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042791-09A-01D_TARGET-15-SJMPAL042791-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL042791-09A-01D_TARGET-15-SJMPAL042791-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042791	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042791-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042791-09A-01D	DNA	EFO	SRS1761116	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042791-09A-01D A59167 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59167	SRX2238824	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042791-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042791-09A-01D A59167 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59167_3_lanes_dupsFlagged_reheadered.bam	SRR4415894	@dbgap@:reads/SRP011999/SRS1761116/SRX2238824/SRR4415894/SRR4415894.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042791-09A-01D_TARGET-15-SJMPAL042791-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL042791-09A-01D_TARGET-15-SJMPAL042791-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042791.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL042791	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042791-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042791-14A-01D	DNA	EFO	SRS1761105	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042791-14A-01D A59276 library	PAIRED	GENOMIC	WGS	RANDOM	440	A59276	SRX2238813	"WGS analysis of normal sample TARGET-15-SJMPAL042791-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL042791-14A-01D A59276 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59276_2_lanes_dupsFlagged_reheadered.bam	SRR4415898	@dbgap@:reads/SRP011999/SRS1761105/SRX2238813/SRR4415898/SRR4415898.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL042791.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042791	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042791-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042791-14A-01D	DNA	EFO	SRS1761105	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042791-14A-01D A59276 library	PAIRED	GENOMIC	WGS	RANDOM	440	A59276	SRX2238813	"WGS analysis of normal sample TARGET-15-SJMPAL042791-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL042791-14A-01D A59276 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59276_2_lanes_dupsFlagged_reheadered.bam	SRR4415898	@dbgap@:reads/SRP011999/SRS1761105/SRX2238813/SRR4415898/SRR4415898.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL042791.quality_tagged.vcf	3						
TARGET-15-SJMPAL042791	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042791-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042791-14A-01D	DNA	EFO	SRS1761105	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042791-14A-01D A59276 library	PAIRED	GENOMIC	WGS	RANDOM	440	A59276	SRX2238813	"WGS analysis of normal sample TARGET-15-SJMPAL042791-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL042791-14A-01D A59276 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59276_2_lanes_dupsFlagged_reheadered.bam	SRR4415898	@dbgap@:reads/SRP011999/SRS1761105/SRX2238813/SRR4415898/SRR4415898.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL042791-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL042791-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042791	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042791-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042791-14A-01D	DNA	EFO	SRS1761105	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042791-14A-01D A59276 library	PAIRED	GENOMIC	WGS	RANDOM	440	A59276	SRX2238813	"WGS analysis of normal sample TARGET-15-SJMPAL042791-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL042791-14A-01D A59276 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59276_2_lanes_dupsFlagged_reheadered.bam	SRR4415898	@dbgap@:reads/SRP011999/SRS1761105/SRX2238813/SRR4415898/SRR4415898.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042791.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042791	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042791-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042791-14A-01D	DNA	EFO	SRS1761105	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042791-14A-01D A59276 library	PAIRED	GENOMIC	WGS	RANDOM	440	A59276	SRX2238813	"WGS analysis of normal sample TARGET-15-SJMPAL042791-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL042791-14A-01D A59276 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59276_2_lanes_dupsFlagged_reheadered.bam	SRR4415898	@dbgap@:reads/SRP011999/SRS1761105/SRX2238813/SRR4415898/SRR4415898.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042791-09A-01D_TARGET-15-SJMPAL042791-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL042791-09A-01D_TARGET-15-SJMPAL042791-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042791	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042791-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042791-14A-01D	DNA	EFO	SRS1761105	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042791-14A-01D A59276 library	PAIRED	GENOMIC	WGS	RANDOM	440	A59276	SRX2238813	"WGS analysis of normal sample TARGET-15-SJMPAL042791-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL042791-14A-01D A59276 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59276_2_lanes_dupsFlagged_reheadered.bam	SRR4415898	@dbgap@:reads/SRP011999/SRS1761105/SRX2238813/SRR4415898/SRR4415898.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042791-09A-01D_TARGET-15-SJMPAL042791-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL042791-09A-01D_TARGET-15-SJMPAL042791-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042791.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL042794	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042794-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042794-09A-01D	DNA	EFO	SRS1761119	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042794-09A-01D A59168 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59168	SRX2238827	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042794-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042794-09A-01D A59168 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59168_3_lanes_dupsFlagged_reheadered.bam	SRR4415851	@dbgap@:reads/SRP011999/SRS1761119/SRX2238827/SRR4415851/SRR4415851.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL042794.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042794	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042794-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042794-09A-01D	DNA	EFO	SRS1761119	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042794-09A-01D A59168 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59168	SRX2238827	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042794-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042794-09A-01D A59168 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59168_3_lanes_dupsFlagged_reheadered.bam	SRR4415851	@dbgap@:reads/SRP011999/SRS1761119/SRX2238827/SRR4415851/SRR4415851.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042794-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL042794.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL042794	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042794-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042794-09A-01D	DNA	EFO	SRS1761119	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042794-09A-01D A59168 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59168	SRX2238827	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042794-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042794-09A-01D A59168 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59168_3_lanes_dupsFlagged_reheadered.bam	SRR4415851	@dbgap@:reads/SRP011999/SRS1761119/SRX2238827/SRR4415851/SRR4415851.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042794-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL042794.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL042794	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042794-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042794-09A-01D	DNA	EFO	SRS1761119	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042794-09A-01D A59168 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59168	SRX2238827	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042794-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042794-09A-01D A59168 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59168_3_lanes_dupsFlagged_reheadered.bam	SRR4415851	@dbgap@:reads/SRP011999/SRS1761119/SRX2238827/SRR4415851/SRR4415851.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042794-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL042794	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042794-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042794-09A-01D	DNA	EFO	SRS1761119	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042794-09A-01D A59168 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59168	SRX2238827	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042794-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042794-09A-01D A59168 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59168_3_lanes_dupsFlagged_reheadered.bam	SRR4415851	@dbgap@:reads/SRP011999/SRS1761119/SRX2238827/SRR4415851/SRR4415851.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL042794.quality_tagged.vcf	3						
TARGET-15-SJMPAL042794	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042794-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042794-09A-01D	DNA	EFO	SRS1761119	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042794-09A-01D A59168 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59168	SRX2238827	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042794-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042794-09A-01D A59168 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59168_3_lanes_dupsFlagged_reheadered.bam	SRR4415851	@dbgap@:reads/SRP011999/SRS1761119/SRX2238827/SRR4415851/SRR4415851.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL042794-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL042794-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042794	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042794-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042794-09A-01D	DNA	EFO	SRS1761119	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042794-09A-01D A59168 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59168	SRX2238827	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042794-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042794-09A-01D A59168 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59168_3_lanes_dupsFlagged_reheadered.bam	SRR4415851	@dbgap@:reads/SRP011999/SRS1761119/SRX2238827/SRR4415851/SRR4415851.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042794.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042794	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042794-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042794-09A-01D	DNA	EFO	SRS1761119	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042794-09A-01D A59168 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59168	SRX2238827	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042794-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042794-09A-01D A59168 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59168_3_lanes_dupsFlagged_reheadered.bam	SRR4415851	@dbgap@:reads/SRP011999/SRS1761119/SRX2238827/SRR4415851/SRR4415851.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042794-09A-01D_TARGET-15-SJMPAL042794-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL042794-09A-01D_TARGET-15-SJMPAL042794-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042794	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042794-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042794-09A-01D	DNA	EFO	SRS1761119	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042794-09A-01D A59168 library	PAIRED	GENOMIC	WGS	RANDOM	476	A59168	SRX2238827	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042794-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL042794-09A-01D A59168 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59168_3_lanes_dupsFlagged_reheadered.bam	SRR4415851	@dbgap@:reads/SRP011999/SRS1761119/SRX2238827/SRR4415851/SRR4415851.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042794-09A-01D_TARGET-15-SJMPAL042794-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL042794-09A-01D_TARGET-15-SJMPAL042794-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042794.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL042794	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042794-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042794-14A.1-01D	DNA	EFO	SRS1761103	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042794-14A.1-01D A59277 library	PAIRED	GENOMIC	WGS	RANDOM	435	A59277	SRX2238811	"WGS analysis of normal sample TARGET-15-SJMPAL042794-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL042794-14A.1-01D A59277 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59277_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634880	@dbgap@:reads/SRP011999/SRS1761103/SRX2238811/SRR5634880/SRR5634880.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL042794.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042794	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042794-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042794-14A.1-01D	DNA	EFO	SRS1761103	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042794-14A.1-01D A59277 library	PAIRED	GENOMIC	WGS	RANDOM	435	A59277	SRX2238811	"WGS analysis of normal sample TARGET-15-SJMPAL042794-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL042794-14A.1-01D A59277 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59277_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634880	@dbgap@:reads/SRP011999/SRS1761103/SRX2238811/SRR5634880/SRR5634880.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL042794.quality_tagged.vcf	3						
TARGET-15-SJMPAL042794	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042794-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042794-14A.1-01D	DNA	EFO	SRS1761103	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042794-14A.1-01D A59277 library	PAIRED	GENOMIC	WGS	RANDOM	435	A59277	SRX2238811	"WGS analysis of normal sample TARGET-15-SJMPAL042794-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL042794-14A.1-01D A59277 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59277_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634880	@dbgap@:reads/SRP011999/SRS1761103/SRX2238811/SRR5634880/SRR5634880.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL042794-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL042794-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042794	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042794-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042794-14A.1-01D	DNA	EFO	SRS1761103	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042794-14A.1-01D A59277 library	PAIRED	GENOMIC	WGS	RANDOM	435	A59277	SRX2238811	"WGS analysis of normal sample TARGET-15-SJMPAL042794-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL042794-14A.1-01D A59277 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59277_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634880	@dbgap@:reads/SRP011999/SRS1761103/SRX2238811/SRR5634880/SRR5634880.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042794.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042794	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042794-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042794-14A.1-01D	DNA	EFO	SRS1761103	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042794-14A.1-01D A59277 library	PAIRED	GENOMIC	WGS	RANDOM	435	A59277	SRX2238811	"WGS analysis of normal sample TARGET-15-SJMPAL042794-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL042794-14A.1-01D A59277 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59277_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634880	@dbgap@:reads/SRP011999/SRS1761103/SRX2238811/SRR5634880/SRR5634880.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042794-09A-01D_TARGET-15-SJMPAL042794-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL042794-09A-01D_TARGET-15-SJMPAL042794-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042794	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042794-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042794-14A.1-01D	DNA	EFO	SRS1761103	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042794-14A.1-01D A59277 library	PAIRED	GENOMIC	WGS	RANDOM	435	A59277	SRX2238811	"WGS analysis of normal sample TARGET-15-SJMPAL042794-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL042794-14A.1-01D A59277 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59277_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634880	@dbgap@:reads/SRP011999/SRS1761103/SRX2238811/SRR5634880/SRR5634880.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042794-09A-01D_TARGET-15-SJMPAL042794-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL042794-09A-01D_TARGET-15-SJMPAL042794-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042794.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL042940	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042940-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042940-03A-01D	DNA	EFO	SRS1761138	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042940-03A-01D A59146 library	PAIRED	GENOMIC	WGS	RANDOM	434	A59146	SRX2238846	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042940-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-26	TARGET-15-SJMPAL042940-03A-01D A59146 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59146_3_lanes_dupsFlagged_reheadered.bam	SRR4415930	@dbgap@:reads/SRP011999/SRS1761138/SRX2238846/SRR4415930/SRR4415930.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL042940.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042940	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042940-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042940-03A-01D	DNA	EFO	SRS1761138	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042940-03A-01D A59146 library	PAIRED	GENOMIC	WGS	RANDOM	434	A59146	SRX2238846	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042940-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-26	TARGET-15-SJMPAL042940-03A-01D A59146 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59146_3_lanes_dupsFlagged_reheadered.bam	SRR4415930	@dbgap@:reads/SRP011999/SRS1761138/SRX2238846/SRR4415930/SRR4415930.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042940-03A-01D.fusion.vcf	3						
TARGET-15-SJMPAL042940	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042940-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042940-03A-01D	DNA	EFO	SRS1761138	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042940-03A-01D A59146 library	PAIRED	GENOMIC	WGS	RANDOM	434	A59146	SRX2238846	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042940-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-26	TARGET-15-SJMPAL042940-03A-01D A59146 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59146_3_lanes_dupsFlagged_reheadered.bam	SRR4415930	@dbgap@:reads/SRP011999/SRS1761138/SRX2238846/SRR4415930/SRR4415930.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042940-03A-01D.indel.vcf	3						
TARGET-15-SJMPAL042940	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042940-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042940-03A-01D	DNA	EFO	SRS1761138	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042940-03A-01D A59146 library	PAIRED	GENOMIC	WGS	RANDOM	434	A59146	SRX2238846	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042940-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-26	TARGET-15-SJMPAL042940-03A-01D A59146 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59146_3_lanes_dupsFlagged_reheadered.bam	SRR4415930	@dbgap@:reads/SRP011999/SRS1761138/SRX2238846/SRR4415930/SRR4415930.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL042940.quality_tagged.vcf	3						
TARGET-15-SJMPAL042940	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042940-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042940-03A-01D	DNA	EFO	SRS1761138	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042940-03A-01D A59146 library	PAIRED	GENOMIC	WGS	RANDOM	434	A59146	SRX2238846	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042940-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-26	TARGET-15-SJMPAL042940-03A-01D A59146 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59146_3_lanes_dupsFlagged_reheadered.bam	SRR4415930	@dbgap@:reads/SRP011999/SRS1761138/SRX2238846/SRR4415930/SRR4415930.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL042940-03A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL042940-03A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042940	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042940-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042940-03A-01D	DNA	EFO	SRS1761138	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042940-03A-01D A59146 library	PAIRED	GENOMIC	WGS	RANDOM	434	A59146	SRX2238846	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042940-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-26	TARGET-15-SJMPAL042940-03A-01D A59146 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59146_3_lanes_dupsFlagged_reheadered.bam	SRR4415930	@dbgap@:reads/SRP011999/SRS1761138/SRX2238846/SRR4415930/SRR4415930.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042940.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042940	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042940-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042940-03A-01D	DNA	EFO	SRS1761138	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042940-03A-01D A59146 library	PAIRED	GENOMIC	WGS	RANDOM	434	A59146	SRX2238846	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042940-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-26	TARGET-15-SJMPAL042940-03A-01D A59146 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59146_3_lanes_dupsFlagged_reheadered.bam	SRR4415930	@dbgap@:reads/SRP011999/SRS1761138/SRX2238846/SRR4415930/SRR4415930.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042940-03A-01D_TARGET-15-SJMPAL042940-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL042940-03A-01D_TARGET-15-SJMPAL042940-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042940	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042940-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042940-03A-01D	DNA	EFO	SRS1761138	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042940-03A-01D A59146 library	PAIRED	GENOMIC	WGS	RANDOM	434	A59146	SRX2238846	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042940-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-26	TARGET-15-SJMPAL042940-03A-01D A59146 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59146_3_lanes_dupsFlagged_reheadered.bam	SRR4415930	@dbgap@:reads/SRP011999/SRS1761138/SRX2238846/SRR4415930/SRR4415930.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042940-03A-01D_TARGET-15-SJMPAL042940-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL042940-03A-01D_TARGET-15-SJMPAL042940-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042940.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL042940	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042940-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042940-14A-01D	DNA	EFO	SRS1761125	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042940-14A-01D A59255 library	PAIRED	GENOMIC	WGS	RANDOM	459	A59255	SRX2238833	"WGS analysis of normal sample TARGET-15-SJMPAL042940-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042940-14A-01D A59255 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59255_2_lanes_dupsFlagged_reheadered.bam	SRR4415842	@dbgap@:reads/SRP011999/SRS1761125/SRX2238833/SRR4415842/SRR4415842.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL042940.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042940	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042940-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042940-14A-01D	DNA	EFO	SRS1761125	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042940-14A-01D A59255 library	PAIRED	GENOMIC	WGS	RANDOM	459	A59255	SRX2238833	"WGS analysis of normal sample TARGET-15-SJMPAL042940-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042940-14A-01D A59255 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59255_2_lanes_dupsFlagged_reheadered.bam	SRR4415842	@dbgap@:reads/SRP011999/SRS1761125/SRX2238833/SRR4415842/SRR4415842.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL042940.quality_tagged.vcf	3						
TARGET-15-SJMPAL042940	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042940-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042940-14A-01D	DNA	EFO	SRS1761125	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042940-14A-01D A59255 library	PAIRED	GENOMIC	WGS	RANDOM	459	A59255	SRX2238833	"WGS analysis of normal sample TARGET-15-SJMPAL042940-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042940-14A-01D A59255 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59255_2_lanes_dupsFlagged_reheadered.bam	SRR4415842	@dbgap@:reads/SRP011999/SRS1761125/SRX2238833/SRR4415842/SRR4415842.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL042940-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL042940-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042940	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042940-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042940-14A-01D	DNA	EFO	SRS1761125	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042940-14A-01D A59255 library	PAIRED	GENOMIC	WGS	RANDOM	459	A59255	SRX2238833	"WGS analysis of normal sample TARGET-15-SJMPAL042940-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042940-14A-01D A59255 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59255_2_lanes_dupsFlagged_reheadered.bam	SRR4415842	@dbgap@:reads/SRP011999/SRS1761125/SRX2238833/SRR4415842/SRR4415842.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042940.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042940	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042940-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042940-14A-01D	DNA	EFO	SRS1761125	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042940-14A-01D A59255 library	PAIRED	GENOMIC	WGS	RANDOM	459	A59255	SRX2238833	"WGS analysis of normal sample TARGET-15-SJMPAL042940-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042940-14A-01D A59255 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59255_2_lanes_dupsFlagged_reheadered.bam	SRR4415842	@dbgap@:reads/SRP011999/SRS1761125/SRX2238833/SRR4415842/SRR4415842.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042940-03A-01D_TARGET-15-SJMPAL042940-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL042940-03A-01D_TARGET-15-SJMPAL042940-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042940	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042940-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042940-14A-01D	DNA	EFO	SRS1761125	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042940-14A-01D A59255 library	PAIRED	GENOMIC	WGS	RANDOM	459	A59255	SRX2238833	"WGS analysis of normal sample TARGET-15-SJMPAL042940-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042940-14A-01D A59255 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59255_2_lanes_dupsFlagged_reheadered.bam	SRR4415842	@dbgap@:reads/SRP011999/SRS1761125/SRX2238833/SRR4415842/SRR4415842.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042940-03A-01D_TARGET-15-SJMPAL042940-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL042940-03A-01D_TARGET-15-SJMPAL042940-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042940.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL042941	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042941-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042941-09A-01D	DNA	EFO	SRS1761202	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042941-09A-01D A59145 library	PAIRED	GENOMIC	WGS	RANDOM	504	A59145	SRX2238909	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042941-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL042941-09A-01D A59145 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59145_3_lanes_dupsFlagged_reheadered.bam	SRR4415916	@dbgap@:reads/SRP011999/SRS1761202/SRX2238909/SRR4415916/SRR4415916.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL042941.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042941	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042941-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042941-09A-01D	DNA	EFO	SRS1761202	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042941-09A-01D A59145 library	PAIRED	GENOMIC	WGS	RANDOM	504	A59145	SRX2238909	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042941-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL042941-09A-01D A59145 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59145_3_lanes_dupsFlagged_reheadered.bam	SRR4415916	@dbgap@:reads/SRP011999/SRS1761202/SRX2238909/SRR4415916/SRR4415916.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042941-09A-01D.fusion.vcf	3						
TARGET-15-SJMPAL042941	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042941-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042941-09A-01D	DNA	EFO	SRS1761202	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042941-09A-01D A59145 library	PAIRED	GENOMIC	WGS	RANDOM	504	A59145	SRX2238909	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042941-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL042941-09A-01D A59145 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59145_3_lanes_dupsFlagged_reheadered.bam	SRR4415916	@dbgap@:reads/SRP011999/SRS1761202/SRX2238909/SRR4415916/SRR4415916.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042941-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL042941	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042941-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042941-09A-01D	DNA	EFO	SRS1761202	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042941-09A-01D A59145 library	PAIRED	GENOMIC	WGS	RANDOM	504	A59145	SRX2238909	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042941-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL042941-09A-01D A59145 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59145_3_lanes_dupsFlagged_reheadered.bam	SRR4415916	@dbgap@:reads/SRP011999/SRS1761202/SRX2238909/SRR4415916/SRR4415916.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL042941.quality_tagged.vcf	3						
TARGET-15-SJMPAL042941	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042941-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042941-09A-01D	DNA	EFO	SRS1761202	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042941-09A-01D A59145 library	PAIRED	GENOMIC	WGS	RANDOM	504	A59145	SRX2238909	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042941-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL042941-09A-01D A59145 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59145_3_lanes_dupsFlagged_reheadered.bam	SRR4415916	@dbgap@:reads/SRP011999/SRS1761202/SRX2238909/SRR4415916/SRR4415916.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL042941-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL042941-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042941	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042941-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042941-09A-01D	DNA	EFO	SRS1761202	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042941-09A-01D A59145 library	PAIRED	GENOMIC	WGS	RANDOM	504	A59145	SRX2238909	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042941-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL042941-09A-01D A59145 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59145_3_lanes_dupsFlagged_reheadered.bam	SRR4415916	@dbgap@:reads/SRP011999/SRS1761202/SRX2238909/SRR4415916/SRR4415916.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042941.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042941	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042941-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042941-09A-01D	DNA	EFO	SRS1761202	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042941-09A-01D A59145 library	PAIRED	GENOMIC	WGS	RANDOM	504	A59145	SRX2238909	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042941-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL042941-09A-01D A59145 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59145_3_lanes_dupsFlagged_reheadered.bam	SRR4415916	@dbgap@:reads/SRP011999/SRS1761202/SRX2238909/SRR4415916/SRR4415916.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042941-09A-01D_TARGET-15-SJMPAL042941-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL042941-09A-01D_TARGET-15-SJMPAL042941-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042941	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042941-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042941-09A-01D	DNA	EFO	SRS1761202	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042941-09A-01D A59145 library	PAIRED	GENOMIC	WGS	RANDOM	504	A59145	SRX2238909	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042941-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL042941-09A-01D A59145 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59145_3_lanes_dupsFlagged_reheadered.bam	SRR4415916	@dbgap@:reads/SRP011999/SRS1761202/SRX2238909/SRR4415916/SRR4415916.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042941-09A-01D_TARGET-15-SJMPAL042941-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL042941-09A-01D_TARGET-15-SJMPAL042941-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042941.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL042941	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042941-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042941-14A-01D	DNA	EFO	SRS1761146	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042941-14A-01D A59254 library	PAIRED	GENOMIC	WGS	RANDOM	442	A59254	SRX2238854	"WGS analysis of normal sample TARGET-15-SJMPAL042941-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042941-14A-01D A59254 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59254_2_lanes_dupsFlagged_reheadered.bam	SRR4415830	@dbgap@:reads/SRP011999/SRS1761146/SRX2238854/SRR4415830/SRR4415830.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL042941.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042941	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042941-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042941-14A-01D	DNA	EFO	SRS1761146	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042941-14A-01D A59254 library	PAIRED	GENOMIC	WGS	RANDOM	442	A59254	SRX2238854	"WGS analysis of normal sample TARGET-15-SJMPAL042941-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042941-14A-01D A59254 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59254_2_lanes_dupsFlagged_reheadered.bam	SRR4415830	@dbgap@:reads/SRP011999/SRS1761146/SRX2238854/SRR4415830/SRR4415830.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL042941.quality_tagged.vcf	3						
TARGET-15-SJMPAL042941	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042941-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042941-14A-01D	DNA	EFO	SRS1761146	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042941-14A-01D A59254 library	PAIRED	GENOMIC	WGS	RANDOM	442	A59254	SRX2238854	"WGS analysis of normal sample TARGET-15-SJMPAL042941-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042941-14A-01D A59254 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59254_2_lanes_dupsFlagged_reheadered.bam	SRR4415830	@dbgap@:reads/SRP011999/SRS1761146/SRX2238854/SRR4415830/SRR4415830.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL042941-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL042941-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042941	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042941-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042941-14A-01D	DNA	EFO	SRS1761146	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042941-14A-01D A59254 library	PAIRED	GENOMIC	WGS	RANDOM	442	A59254	SRX2238854	"WGS analysis of normal sample TARGET-15-SJMPAL042941-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042941-14A-01D A59254 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59254_2_lanes_dupsFlagged_reheadered.bam	SRR4415830	@dbgap@:reads/SRP011999/SRS1761146/SRX2238854/SRR4415830/SRR4415830.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042941.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042941	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042941-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042941-14A-01D	DNA	EFO	SRS1761146	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042941-14A-01D A59254 library	PAIRED	GENOMIC	WGS	RANDOM	442	A59254	SRX2238854	"WGS analysis of normal sample TARGET-15-SJMPAL042941-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042941-14A-01D A59254 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59254_2_lanes_dupsFlagged_reheadered.bam	SRR4415830	@dbgap@:reads/SRP011999/SRS1761146/SRX2238854/SRR4415830/SRR4415830.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042941-09A-01D_TARGET-15-SJMPAL042941-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL042941-09A-01D_TARGET-15-SJMPAL042941-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042941	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042941-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042941-14A-01D	DNA	EFO	SRS1761146	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042941-14A-01D A59254 library	PAIRED	GENOMIC	WGS	RANDOM	442	A59254	SRX2238854	"WGS analysis of normal sample TARGET-15-SJMPAL042941-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042941-14A-01D A59254 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59254_2_lanes_dupsFlagged_reheadered.bam	SRR4415830	@dbgap@:reads/SRP011999/SRS1761146/SRX2238854/SRR4415830/SRR4415830.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042941-09A-01D_TARGET-15-SJMPAL042941-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL042941-09A-01D_TARGET-15-SJMPAL042941-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042941.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL042942	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042942-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042942-09A-01D	DNA	EFO	SRS1761179	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042942-09A-01D A59148 library	PAIRED	GENOMIC	WGS	RANDOM	479	A59148	SRX2238887	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042942-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL042942-09A-01D A59148 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59148_3_lanes_dupsFlagged_reheadered.bam	SRR4415870	@dbgap@:reads/SRP011999/SRS1761179/SRX2238887/SRR4415870/SRR4415870.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL042942.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042942	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042942-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042942-09A-01D	DNA	EFO	SRS1761179	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042942-09A-01D A59148 library	PAIRED	GENOMIC	WGS	RANDOM	479	A59148	SRX2238887	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042942-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL042942-09A-01D A59148 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59148_3_lanes_dupsFlagged_reheadered.bam	SRR4415870	@dbgap@:reads/SRP011999/SRS1761179/SRX2238887/SRR4415870/SRR4415870.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042942-09A-01D.fusion.vcf	3						
TARGET-15-SJMPAL042942	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042942-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042942-09A-01D	DNA	EFO	SRS1761179	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042942-09A-01D A59148 library	PAIRED	GENOMIC	WGS	RANDOM	479	A59148	SRX2238887	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042942-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL042942-09A-01D A59148 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59148_3_lanes_dupsFlagged_reheadered.bam	SRR4415870	@dbgap@:reads/SRP011999/SRS1761179/SRX2238887/SRR4415870/SRR4415870.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042942-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL042942	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042942-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042942-09A-01D	DNA	EFO	SRS1761179	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042942-09A-01D A59148 library	PAIRED	GENOMIC	WGS	RANDOM	479	A59148	SRX2238887	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042942-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL042942-09A-01D A59148 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59148_3_lanes_dupsFlagged_reheadered.bam	SRR4415870	@dbgap@:reads/SRP011999/SRS1761179/SRX2238887/SRR4415870/SRR4415870.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL042942.quality_tagged.vcf	3						
TARGET-15-SJMPAL042942	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042942-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042942-09A-01D	DNA	EFO	SRS1761179	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042942-09A-01D A59148 library	PAIRED	GENOMIC	WGS	RANDOM	479	A59148	SRX2238887	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042942-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL042942-09A-01D A59148 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59148_3_lanes_dupsFlagged_reheadered.bam	SRR4415870	@dbgap@:reads/SRP011999/SRS1761179/SRX2238887/SRR4415870/SRR4415870.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL042942-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL042942-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042942	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042942-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042942-09A-01D	DNA	EFO	SRS1761179	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042942-09A-01D A59148 library	PAIRED	GENOMIC	WGS	RANDOM	479	A59148	SRX2238887	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042942-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL042942-09A-01D A59148 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59148_3_lanes_dupsFlagged_reheadered.bam	SRR4415870	@dbgap@:reads/SRP011999/SRS1761179/SRX2238887/SRR4415870/SRR4415870.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042942.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042942	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042942-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042942-09A-01D	DNA	EFO	SRS1761179	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042942-09A-01D A59148 library	PAIRED	GENOMIC	WGS	RANDOM	479	A59148	SRX2238887	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042942-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL042942-09A-01D A59148 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59148_3_lanes_dupsFlagged_reheadered.bam	SRR4415870	@dbgap@:reads/SRP011999/SRS1761179/SRX2238887/SRR4415870/SRR4415870.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042942-09A-01D_TARGET-15-SJMPAL042942-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL042942-09A-01D_TARGET-15-SJMPAL042942-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042942	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042942-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042942-09A-01D	DNA	EFO	SRS1761179	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042942-09A-01D A59148 library	PAIRED	GENOMIC	WGS	RANDOM	479	A59148	SRX2238887	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042942-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL042942-09A-01D A59148 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59148_3_lanes_dupsFlagged_reheadered.bam	SRR4415870	@dbgap@:reads/SRP011999/SRS1761179/SRX2238887/SRR4415870/SRR4415870.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042942-09A-01D_TARGET-15-SJMPAL042942-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL042942-09A-01D_TARGET-15-SJMPAL042942-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042942.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL042942	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042942-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042942-14A-01D	DNA	EFO	SRS1761201	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042942-14A-01D A59257 library	PAIRED	GENOMIC	WGS	RANDOM	444	A59257	SRX2238910	"WGS analysis of normal sample TARGET-15-SJMPAL042942-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL042942-14A-01D A59257 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59257_2_lanes_dupsFlagged_reheadered.bam	SRR4415879	@dbgap@:reads/SRP011999/SRS1761201/SRX2238910/SRR4415879/SRR4415879.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL042942.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042942	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042942-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042942-14A-01D	DNA	EFO	SRS1761201	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042942-14A-01D A59257 library	PAIRED	GENOMIC	WGS	RANDOM	444	A59257	SRX2238910	"WGS analysis of normal sample TARGET-15-SJMPAL042942-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL042942-14A-01D A59257 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59257_2_lanes_dupsFlagged_reheadered.bam	SRR4415879	@dbgap@:reads/SRP011999/SRS1761201/SRX2238910/SRR4415879/SRR4415879.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL042942.quality_tagged.vcf	3						
TARGET-15-SJMPAL042942	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042942-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042942-14A-01D	DNA	EFO	SRS1761201	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042942-14A-01D A59257 library	PAIRED	GENOMIC	WGS	RANDOM	444	A59257	SRX2238910	"WGS analysis of normal sample TARGET-15-SJMPAL042942-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL042942-14A-01D A59257 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59257_2_lanes_dupsFlagged_reheadered.bam	SRR4415879	@dbgap@:reads/SRP011999/SRS1761201/SRX2238910/SRR4415879/SRR4415879.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL042942-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL042942-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042942	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042942-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042942-14A-01D	DNA	EFO	SRS1761201	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042942-14A-01D A59257 library	PAIRED	GENOMIC	WGS	RANDOM	444	A59257	SRX2238910	"WGS analysis of normal sample TARGET-15-SJMPAL042942-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL042942-14A-01D A59257 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59257_2_lanes_dupsFlagged_reheadered.bam	SRR4415879	@dbgap@:reads/SRP011999/SRS1761201/SRX2238910/SRR4415879/SRR4415879.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042942.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042942	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042942-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042942-14A-01D	DNA	EFO	SRS1761201	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042942-14A-01D A59257 library	PAIRED	GENOMIC	WGS	RANDOM	444	A59257	SRX2238910	"WGS analysis of normal sample TARGET-15-SJMPAL042942-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL042942-14A-01D A59257 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59257_2_lanes_dupsFlagged_reheadered.bam	SRR4415879	@dbgap@:reads/SRP011999/SRS1761201/SRX2238910/SRR4415879/SRR4415879.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042942-09A-01D_TARGET-15-SJMPAL042942-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL042942-09A-01D_TARGET-15-SJMPAL042942-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042942	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042942-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042942-14A-01D	DNA	EFO	SRS1761201	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042942-14A-01D A59257 library	PAIRED	GENOMIC	WGS	RANDOM	444	A59257	SRX2238910	"WGS analysis of normal sample TARGET-15-SJMPAL042942-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL042942-14A-01D A59257 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59257_2_lanes_dupsFlagged_reheadered.bam	SRR4415879	@dbgap@:reads/SRP011999/SRS1761201/SRX2238910/SRR4415879/SRR4415879.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042942-09A-01D_TARGET-15-SJMPAL042942-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL042942-09A-01D_TARGET-15-SJMPAL042942-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042942.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-04A-01D	DNA	EFO	SRS1761158	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-04A-01D A59130 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59130	SRX2238866	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042946-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL042946-04A-01D A59130 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59130_3_lanes_dupsFlagged_reheadered.bam	SRR4415875	@dbgap@:reads/SRP011999/SRS1761158/SRX2238866/SRR4415875/SRR4415875.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL042946.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-04A-01D	DNA	EFO	SRS1761158	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-04A-01D A59130 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59130	SRX2238866	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042946-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL042946-04A-01D A59130 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59130_3_lanes_dupsFlagged_reheadered.bam	SRR4415875	@dbgap@:reads/SRP011999/SRS1761158/SRX2238866/SRR4415875/SRR4415875.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042946-04A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL042946.gv2.relapse.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-04A-01D	DNA	EFO	SRS1761158	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-04A-01D A59130 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59130	SRX2238866	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042946-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL042946-04A-01D A59130 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59130_3_lanes_dupsFlagged_reheadered.bam	SRR4415875	@dbgap@:reads/SRP011999/SRS1761158/SRX2238866/SRR4415875/SRR4415875.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042946-04A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL042946.gv2.relapse.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-04A-01D	DNA	EFO	SRS1761158	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-04A-01D A59130 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59130	SRX2238866	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042946-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL042946-04A-01D A59130 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59130_3_lanes_dupsFlagged_reheadered.bam	SRR4415875	@dbgap@:reads/SRP011999/SRS1761158/SRX2238866/SRR4415875/SRR4415875.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042946-04A-01D.indel.vcf	3						
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-04A-01D	DNA	EFO	SRS1761158	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-04A-01D A59130 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59130	SRX2238866	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042946-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL042946-04A-01D A59130 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59130_3_lanes_dupsFlagged_reheadered.bam	SRR4415875	@dbgap@:reads/SRP011999/SRS1761158/SRX2238866/SRR4415875/SRR4415875.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL042946.quality_tagged.vcf	3						
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-04A-01D	DNA	EFO	SRS1761158	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-04A-01D A59130 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59130	SRX2238866	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042946-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL042946-04A-01D A59130 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59130_3_lanes_dupsFlagged_reheadered.bam	SRR4415875	@dbgap@:reads/SRP011999/SRS1761158/SRX2238866/SRR4415875/SRR4415875.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL042946-04A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL042946-04A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-04A-01D	DNA	EFO	SRS1761158	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-04A-01D A59130 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59130	SRX2238866	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042946-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL042946-04A-01D A59130 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59130_3_lanes_dupsFlagged_reheadered.bam	SRR4415875	@dbgap@:reads/SRP011999/SRS1761158/SRX2238866/SRR4415875/SRR4415875.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042946.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-04A-01D	DNA	EFO	SRS1761158	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-04A-01D A59130 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59130	SRX2238866	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042946-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL042946-04A-01D A59130 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59130_3_lanes_dupsFlagged_reheadered.bam	SRR4415875	@dbgap@:reads/SRP011999/SRS1761158/SRX2238866/SRR4415875/SRR4415875.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042946-04A-01D_TARGET-15-SJMPAL042946-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL042946-04A-01D_TARGET-15-SJMPAL042946-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-04A-01D	DNA	EFO	SRS1761158	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-04A-01D A59130 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59130	SRX2238866	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042946-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL042946-04A-01D A59130 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59130_3_lanes_dupsFlagged_reheadered.bam	SRR4415875	@dbgap@:reads/SRP011999/SRS1761158/SRX2238866/SRR4415875/SRR4415875.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042946-04A-01D_TARGET-15-SJMPAL042946-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL042946-04A-01D_TARGET-15-SJMPAL042946-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042946.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-09A-01D	DNA	EFO	SRS1761204	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-09A-01D A59129 library	PAIRED	GENOMIC	WGS	RANDOM	495	A59129	SRX2238912	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042946-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL042946-09A-01D A59129 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59129_3_lanes_dupsFlagged_reheadered.bam	SRR4415918	@dbgap@:reads/SRP011999/SRS1761204/SRX2238912/SRR4415918/SRR4415918.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL042946.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-09A-01D	DNA	EFO	SRS1761204	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-09A-01D A59129 library	PAIRED	GENOMIC	WGS	RANDOM	495	A59129	SRX2238912	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042946-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL042946-09A-01D A59129 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59129_3_lanes_dupsFlagged_reheadered.bam	SRR4415918	@dbgap@:reads/SRP011999/SRS1761204/SRX2238912/SRR4415918/SRR4415918.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042946-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL042946.gv2.primary.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-09A-01D	DNA	EFO	SRS1761204	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-09A-01D A59129 library	PAIRED	GENOMIC	WGS	RANDOM	495	A59129	SRX2238912	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042946-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL042946-09A-01D A59129 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59129_3_lanes_dupsFlagged_reheadered.bam	SRR4415918	@dbgap@:reads/SRP011999/SRS1761204/SRX2238912/SRR4415918/SRR4415918.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042946-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL042946.gv2.primary.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-09A-01D	DNA	EFO	SRS1761204	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-09A-01D A59129 library	PAIRED	GENOMIC	WGS	RANDOM	495	A59129	SRX2238912	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042946-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL042946-09A-01D A59129 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59129_3_lanes_dupsFlagged_reheadered.bam	SRR4415918	@dbgap@:reads/SRP011999/SRS1761204/SRX2238912/SRR4415918/SRR4415918.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL042946-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-09A-01D	DNA	EFO	SRS1761204	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-09A-01D A59129 library	PAIRED	GENOMIC	WGS	RANDOM	495	A59129	SRX2238912	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042946-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL042946-09A-01D A59129 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59129_3_lanes_dupsFlagged_reheadered.bam	SRR4415918	@dbgap@:reads/SRP011999/SRS1761204/SRX2238912/SRR4415918/SRR4415918.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL042946.quality_tagged.vcf	3						
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-09A-01D	DNA	EFO	SRS1761204	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-09A-01D A59129 library	PAIRED	GENOMIC	WGS	RANDOM	495	A59129	SRX2238912	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042946-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL042946-09A-01D A59129 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59129_3_lanes_dupsFlagged_reheadered.bam	SRR4415918	@dbgap@:reads/SRP011999/SRS1761204/SRX2238912/SRR4415918/SRR4415918.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL042946-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL042946-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-09A-01D	DNA	EFO	SRS1761204	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-09A-01D A59129 library	PAIRED	GENOMIC	WGS	RANDOM	495	A59129	SRX2238912	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042946-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL042946-09A-01D A59129 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59129_3_lanes_dupsFlagged_reheadered.bam	SRR4415918	@dbgap@:reads/SRP011999/SRS1761204/SRX2238912/SRR4415918/SRR4415918.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042946.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-09A-01D	DNA	EFO	SRS1761204	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-09A-01D A59129 library	PAIRED	GENOMIC	WGS	RANDOM	495	A59129	SRX2238912	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042946-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL042946-09A-01D A59129 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59129_3_lanes_dupsFlagged_reheadered.bam	SRR4415918	@dbgap@:reads/SRP011999/SRS1761204/SRX2238912/SRR4415918/SRR4415918.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042946-09A-01D_TARGET-15-SJMPAL042946-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL042946-09A-01D_TARGET-15-SJMPAL042946-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-09A-01D	DNA	EFO	SRS1761204	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-09A-01D A59129 library	PAIRED	GENOMIC	WGS	RANDOM	495	A59129	SRX2238912	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL042946-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL042946-09A-01D A59129 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59129_3_lanes_dupsFlagged_reheadered.bam	SRR4415918	@dbgap@:reads/SRP011999/SRS1761204/SRX2238912/SRR4415918/SRR4415918.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042946-09A-01D_TARGET-15-SJMPAL042946-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL042946-09A-01D_TARGET-15-SJMPAL042946-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042946.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-14A.1-01D	DNA	EFO	SRS1761181	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-14A.1-01D A59239 library	PAIRED	GENOMIC	WGS	RANDOM	433	A59239	SRX2238889	"WGS analysis of normal sample TARGET-15-SJMPAL042946-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042946-14A.1-01D A59239 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59239_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634853	@dbgap@:reads/SRP011999/SRS1761181/SRX2238889/SRR5634853/SRR5634853.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL042946.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-14A.1-01D	DNA	EFO	SRS1761181	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-14A.1-01D A59239 library	PAIRED	GENOMIC	WGS	RANDOM	433	A59239	SRX2238889	"WGS analysis of normal sample TARGET-15-SJMPAL042946-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042946-14A.1-01D A59239 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59239_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634853	@dbgap@:reads/SRP011999/SRS1761181/SRX2238889/SRR5634853/SRR5634853.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL042946.quality_tagged.vcf	3						
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-14A.1-01D	DNA	EFO	SRS1761181	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-14A.1-01D A59239 library	PAIRED	GENOMIC	WGS	RANDOM	433	A59239	SRX2238889	"WGS analysis of normal sample TARGET-15-SJMPAL042946-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042946-14A.1-01D A59239 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59239_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634853	@dbgap@:reads/SRP011999/SRS1761181/SRX2238889/SRR5634853/SRR5634853.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL042946-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL042946-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-14A.1-01D	DNA	EFO	SRS1761181	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-14A.1-01D A59239 library	PAIRED	GENOMIC	WGS	RANDOM	433	A59239	SRX2238889	"WGS analysis of normal sample TARGET-15-SJMPAL042946-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042946-14A.1-01D A59239 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59239_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634853	@dbgap@:reads/SRP011999/SRS1761181/SRX2238889/SRR5634853/SRR5634853.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042946.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-14A.1-01D	DNA	EFO	SRS1761181	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-14A.1-01D A59239 library	PAIRED	GENOMIC	WGS	RANDOM	433	A59239	SRX2238889	"WGS analysis of normal sample TARGET-15-SJMPAL042946-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042946-14A.1-01D A59239 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59239_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634853	@dbgap@:reads/SRP011999/SRS1761181/SRX2238889/SRR5634853/SRR5634853.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042946-04A-01D_TARGET-15-SJMPAL042946-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL042946-04A-01D_TARGET-15-SJMPAL042946-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-14A.1-01D	DNA	EFO	SRS1761181	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-14A.1-01D A59239 library	PAIRED	GENOMIC	WGS	RANDOM	433	A59239	SRX2238889	"WGS analysis of normal sample TARGET-15-SJMPAL042946-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042946-14A.1-01D A59239 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59239_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634853	@dbgap@:reads/SRP011999/SRS1761181/SRX2238889/SRR5634853/SRR5634853.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042946-04A-01D_TARGET-15-SJMPAL042946-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL042946-04A-01D_TARGET-15-SJMPAL042946-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042946.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-14A.1-01D	DNA	EFO	SRS1761181	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-14A.1-01D A59239 library	PAIRED	GENOMIC	WGS	RANDOM	433	A59239	SRX2238889	"WGS analysis of normal sample TARGET-15-SJMPAL042946-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042946-14A.1-01D A59239 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59239_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634853	@dbgap@:reads/SRP011999/SRS1761181/SRX2238889/SRR5634853/SRR5634853.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042946-09A-01D_TARGET-15-SJMPAL042946-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL042946-09A-01D_TARGET-15-SJMPAL042946-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL042946	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL042946-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL042946-14A.1-01D	DNA	EFO	SRS1761181	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL042946-14A.1-01D A59239 library	PAIRED	GENOMIC	WGS	RANDOM	433	A59239	SRX2238889	"WGS analysis of normal sample TARGET-15-SJMPAL042946-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL042946-14A.1-01D A59239 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59239_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634853	@dbgap@:reads/SRP011999/SRS1761181/SRX2238889/SRR5634853/SRR5634853.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL042946-09A-01D_TARGET-15-SJMPAL042946-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL042946-09A-01D_TARGET-15-SJMPAL042946-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL042946.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.1-01D	DNA	EFO	SRS1761169	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.1-01D A59169 library	PAIRED	GENOMIC	WGS	RANDOM	490	A59169	SRX2238877	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL043505-09A.1-01D A59169 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59169_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634850	@dbgap@:reads/SRP011999/SRS1761169/SRX2238877/SRR5634850/SRR5634850.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043505.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.1-01D	DNA	EFO	SRS1761169	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.1-01D A59169 library	PAIRED	GENOMIC	WGS	RANDOM	490	A59169	SRX2238877	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL043505-09A.1-01D A59169 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59169_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634850	@dbgap@:reads/SRP011999/SRS1761169/SRX2238877/SRR5634850/SRR5634850.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043505-09A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043505.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.1-01D	DNA	EFO	SRS1761169	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.1-01D A59169 library	PAIRED	GENOMIC	WGS	RANDOM	490	A59169	SRX2238877	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL043505-09A.1-01D A59169 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59169_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634850	@dbgap@:reads/SRP011999/SRS1761169/SRX2238877/SRR5634850/SRR5634850.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043505-09A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043505.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.1-01D	DNA	EFO	SRS1761169	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.1-01D A59169 library	PAIRED	GENOMIC	WGS	RANDOM	490	A59169	SRX2238877	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL043505-09A.1-01D A59169 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59169_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634850	@dbgap@:reads/SRP011999/SRS1761169/SRX2238877/SRR5634850/SRR5634850.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043505-09A.1-01D.indel.vcf	3						
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.1-01D	DNA	EFO	SRS1761169	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.1-01D A59169 library	PAIRED	GENOMIC	WGS	RANDOM	490	A59169	SRX2238877	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL043505-09A.1-01D A59169 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59169_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634850	@dbgap@:reads/SRP011999/SRS1761169/SRX2238877/SRR5634850/SRR5634850.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043505.quality_tagged.vcf	3						
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.1-01D	DNA	EFO	SRS1761169	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.1-01D A59169 library	PAIRED	GENOMIC	WGS	RANDOM	490	A59169	SRX2238877	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL043505-09A.1-01D A59169 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59169_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634850	@dbgap@:reads/SRP011999/SRS1761169/SRX2238877/SRR5634850/SRR5634850.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043505-09A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043505-09A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.1-01D	DNA	EFO	SRS1761169	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.1-01D A59169 library	PAIRED	GENOMIC	WGS	RANDOM	490	A59169	SRX2238877	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL043505-09A.1-01D A59169 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59169_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634850	@dbgap@:reads/SRP011999/SRS1761169/SRX2238877/SRR5634850/SRR5634850.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043505.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.1-01D	DNA	EFO	SRS1761169	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.1-01D A59169 library	PAIRED	GENOMIC	WGS	RANDOM	490	A59169	SRX2238877	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL043505-09A.1-01D A59169 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59169_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634850	@dbgap@:reads/SRP011999/SRS1761169/SRX2238877/SRR5634850/SRR5634850.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043505-09A.1-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043505-09A.1-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.1-01D	DNA	EFO	SRS1761169	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.1-01D A59169 library	PAIRED	GENOMIC	WGS	RANDOM	490	A59169	SRX2238877	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-05	TARGET-15-SJMPAL043505-09A.1-01D A59169 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59169_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634850	@dbgap@:reads/SRP011999/SRS1761169/SRX2238877/SRR5634850/SRR5634850.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043505-09A.1-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043505-09A.1-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043505.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.2-01D	DNA	EFO	SRS1761153	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.2-01D A59170 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59170	SRX2238860	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043505-09A.2-01D A59170 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59170_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634868	@dbgap@:reads/SRP011999/SRS1761153/SRX2238860/SRR5634868/SRR5634868.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043505.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.2-01D	DNA	EFO	SRS1761153	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.2-01D A59170 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59170	SRX2238860	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043505-09A.2-01D A59170 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59170_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634868	@dbgap@:reads/SRP011999/SRS1761153/SRX2238860/SRR5634868/SRR5634868.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043505-09A.2-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043505.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.2-01D	DNA	EFO	SRS1761153	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.2-01D A59170 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59170	SRX2238860	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043505-09A.2-01D A59170 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59170_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634868	@dbgap@:reads/SRP011999/SRS1761153/SRX2238860/SRR5634868/SRR5634868.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043505-09A.2-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043505.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.2-01D	DNA	EFO	SRS1761153	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.2-01D A59170 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59170	SRX2238860	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043505-09A.2-01D A59170 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59170_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634868	@dbgap@:reads/SRP011999/SRS1761153/SRX2238860/SRR5634868/SRR5634868.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043505-09A.2-01D.indel.vcf	3						
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.2-01D	DNA	EFO	SRS1761153	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.2-01D A59170 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59170	SRX2238860	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043505-09A.2-01D A59170 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59170_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634868	@dbgap@:reads/SRP011999/SRS1761153/SRX2238860/SRR5634868/SRR5634868.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043505.quality_tagged.vcf	3						
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.2-01D	DNA	EFO	SRS1761153	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.2-01D A59170 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59170	SRX2238860	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043505-09A.2-01D A59170 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59170_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634868	@dbgap@:reads/SRP011999/SRS1761153/SRX2238860/SRR5634868/SRR5634868.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043505-09A.2-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043505-09A.2-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.2-01D	DNA	EFO	SRS1761153	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.2-01D A59170 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59170	SRX2238860	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043505-09A.2-01D A59170 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59170_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634868	@dbgap@:reads/SRP011999/SRS1761153/SRX2238860/SRR5634868/SRR5634868.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043505.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.2-01D	DNA	EFO	SRS1761153	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.2-01D A59170 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59170	SRX2238860	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043505-09A.2-01D A59170 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59170_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634868	@dbgap@:reads/SRP011999/SRS1761153/SRX2238860/SRR5634868/SRR5634868.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043505-09A.2-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043505-09A.2-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.2	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.2-01D	DNA	EFO	SRS1761153	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.2-01D A59170 library	PAIRED	GENOMIC	WGS	RANDOM	496	A59170	SRX2238860	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.2-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043505-09A.2-01D A59170 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59170_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634868	@dbgap@:reads/SRP011999/SRS1761153/SRX2238860/SRR5634868/SRR5634868.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043505-09A.2-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043505-09A.2-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043505.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.3-01D	DNA	EFO	SRS1761109	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.3-01D A59171 library	PAIRED	GENOMIC	WGS	RANDOM	451	A59171	SRX2238817	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043505-09A.3-01D A59171 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59171_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634828	@dbgap@:reads/SRP011999/SRS1761109/SRX2238817/SRR5634828/SRR5634828.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043505.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.3-01D	DNA	EFO	SRS1761109	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.3-01D A59171 library	PAIRED	GENOMIC	WGS	RANDOM	451	A59171	SRX2238817	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043505-09A.3-01D A59171 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59171_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634828	@dbgap@:reads/SRP011999/SRS1761109/SRX2238817/SRR5634828/SRR5634828.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043505-09A.3-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043505.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.3-01D	DNA	EFO	SRS1761109	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.3-01D A59171 library	PAIRED	GENOMIC	WGS	RANDOM	451	A59171	SRX2238817	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043505-09A.3-01D A59171 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59171_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634828	@dbgap@:reads/SRP011999/SRS1761109/SRX2238817/SRR5634828/SRR5634828.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043505-09A.3-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043505.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.3-01D	DNA	EFO	SRS1761109	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.3-01D A59171 library	PAIRED	GENOMIC	WGS	RANDOM	451	A59171	SRX2238817	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043505-09A.3-01D A59171 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59171_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634828	@dbgap@:reads/SRP011999/SRS1761109/SRX2238817/SRR5634828/SRR5634828.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043505-09A.3-01D.indel.vcf	3						
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.3-01D	DNA	EFO	SRS1761109	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.3-01D A59171 library	PAIRED	GENOMIC	WGS	RANDOM	451	A59171	SRX2238817	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043505-09A.3-01D A59171 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59171_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634828	@dbgap@:reads/SRP011999/SRS1761109/SRX2238817/SRR5634828/SRR5634828.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043505.quality_tagged.vcf	3						
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.3-01D	DNA	EFO	SRS1761109	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.3-01D A59171 library	PAIRED	GENOMIC	WGS	RANDOM	451	A59171	SRX2238817	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043505-09A.3-01D A59171 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59171_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634828	@dbgap@:reads/SRP011999/SRS1761109/SRX2238817/SRR5634828/SRR5634828.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043505-09A.3-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043505-09A.3-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.3-01D	DNA	EFO	SRS1761109	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.3-01D A59171 library	PAIRED	GENOMIC	WGS	RANDOM	451	A59171	SRX2238817	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043505-09A.3-01D A59171 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59171_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634828	@dbgap@:reads/SRP011999/SRS1761109/SRX2238817/SRR5634828/SRR5634828.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043505.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.3-01D	DNA	EFO	SRS1761109	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.3-01D A59171 library	PAIRED	GENOMIC	WGS	RANDOM	451	A59171	SRX2238817	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043505-09A.3-01D A59171 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59171_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634828	@dbgap@:reads/SRP011999/SRS1761109/SRX2238817/SRR5634828/SRR5634828.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043505-09A.3-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043505-09A.3-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-09A.3	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-09A.3-01D	DNA	EFO	SRS1761109	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-09A.3-01D A59171 library	PAIRED	GENOMIC	WGS	RANDOM	451	A59171	SRX2238817	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043505-09A.3-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043505-09A.3-01D A59171 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59171_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634828	@dbgap@:reads/SRP011999/SRS1761109/SRX2238817/SRR5634828/SRR5634828.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043505-09A.3-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043505-09A.3-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043505.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-14A-01D	DNA	EFO	SRS1761118	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-14A-01D A59278 library	PAIRED	GENOMIC	WGS	RANDOM	449	A59278	SRX2238826	"WGS analysis of normal sample TARGET-15-SJMPAL043505-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL043505-14A-01D A59278 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59278_2_lanes_dupsFlagged_reheadered.bam	SRR4415902	@dbgap@:reads/SRP011999/SRS1761118/SRX2238826/SRR4415902/SRR4415902.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043505.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-14A-01D	DNA	EFO	SRS1761118	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-14A-01D A59278 library	PAIRED	GENOMIC	WGS	RANDOM	449	A59278	SRX2238826	"WGS analysis of normal sample TARGET-15-SJMPAL043505-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL043505-14A-01D A59278 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59278_2_lanes_dupsFlagged_reheadered.bam	SRR4415902	@dbgap@:reads/SRP011999/SRS1761118/SRX2238826/SRR4415902/SRR4415902.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043505.quality_tagged.vcf	3						
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-14A-01D	DNA	EFO	SRS1761118	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-14A-01D A59278 library	PAIRED	GENOMIC	WGS	RANDOM	449	A59278	SRX2238826	"WGS analysis of normal sample TARGET-15-SJMPAL043505-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL043505-14A-01D A59278 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59278_2_lanes_dupsFlagged_reheadered.bam	SRR4415902	@dbgap@:reads/SRP011999/SRS1761118/SRX2238826/SRR4415902/SRR4415902.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043505-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043505-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-14A-01D	DNA	EFO	SRS1761118	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-14A-01D A59278 library	PAIRED	GENOMIC	WGS	RANDOM	449	A59278	SRX2238826	"WGS analysis of normal sample TARGET-15-SJMPAL043505-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL043505-14A-01D A59278 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59278_2_lanes_dupsFlagged_reheadered.bam	SRR4415902	@dbgap@:reads/SRP011999/SRS1761118/SRX2238826/SRR4415902/SRR4415902.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043505.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-14A-01D	DNA	EFO	SRS1761118	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-14A-01D A59278 library	PAIRED	GENOMIC	WGS	RANDOM	449	A59278	SRX2238826	"WGS analysis of normal sample TARGET-15-SJMPAL043505-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL043505-14A-01D A59278 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59278_2_lanes_dupsFlagged_reheadered.bam	SRR4415902	@dbgap@:reads/SRP011999/SRS1761118/SRX2238826/SRR4415902/SRR4415902.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043505-09A.1-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043505-09A.1-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-14A-01D	DNA	EFO	SRS1761118	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-14A-01D A59278 library	PAIRED	GENOMIC	WGS	RANDOM	449	A59278	SRX2238826	"WGS analysis of normal sample TARGET-15-SJMPAL043505-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL043505-14A-01D A59278 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59278_2_lanes_dupsFlagged_reheadered.bam	SRR4415902	@dbgap@:reads/SRP011999/SRS1761118/SRX2238826/SRR4415902/SRR4415902.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043505-09A.1-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043505-09A.1-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043505.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-14A-01D	DNA	EFO	SRS1761118	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-14A-01D A59278 library	PAIRED	GENOMIC	WGS	RANDOM	449	A59278	SRX2238826	"WGS analysis of normal sample TARGET-15-SJMPAL043505-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL043505-14A-01D A59278 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59278_2_lanes_dupsFlagged_reheadered.bam	SRR4415902	@dbgap@:reads/SRP011999/SRS1761118/SRX2238826/SRR4415902/SRR4415902.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043505-09A.2-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043505-09A.2-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-14A-01D	DNA	EFO	SRS1761118	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-14A-01D A59278 library	PAIRED	GENOMIC	WGS	RANDOM	449	A59278	SRX2238826	"WGS analysis of normal sample TARGET-15-SJMPAL043505-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL043505-14A-01D A59278 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59278_2_lanes_dupsFlagged_reheadered.bam	SRR4415902	@dbgap@:reads/SRP011999/SRS1761118/SRX2238826/SRR4415902/SRR4415902.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043505-09A.2-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043505-09A.2-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043505.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-14A-01D	DNA	EFO	SRS1761118	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-14A-01D A59278 library	PAIRED	GENOMIC	WGS	RANDOM	449	A59278	SRX2238826	"WGS analysis of normal sample TARGET-15-SJMPAL043505-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL043505-14A-01D A59278 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59278_2_lanes_dupsFlagged_reheadered.bam	SRR4415902	@dbgap@:reads/SRP011999/SRS1761118/SRX2238826/SRR4415902/SRR4415902.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043505-09A.3-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043505-09A.3-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043505	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043505-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043505-14A-01D	DNA	EFO	SRS1761118	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043505-14A-01D A59278 library	PAIRED	GENOMIC	WGS	RANDOM	449	A59278	SRX2238826	"WGS analysis of normal sample TARGET-15-SJMPAL043505-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-16	TARGET-15-SJMPAL043505-14A-01D A59278 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59278_2_lanes_dupsFlagged_reheadered.bam	SRR4415902	@dbgap@:reads/SRP011999/SRS1761118/SRX2238826/SRR4415902/SRR4415902.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043505-09A.3-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043505-09A.3-01D_TARGET-15-SJMPAL043505-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043505.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043506	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043506-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043506-04A-01D	DNA	EFO	SRS1761171	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043506-04A-01D A59127 library	PAIRED	GENOMIC	WGS	RANDOM	482	A59127	SRX2238879	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043506-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL043506-04A-01D A59127 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59127_3_lanes_dupsFlagged_reheadered.bam	SRR4415861	@dbgap@:reads/SRP011999/SRS1761171/SRX2238879/SRR4415861/SRR4415861.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043506.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043506	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043506-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043506-04A-01D	DNA	EFO	SRS1761171	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043506-04A-01D A59127 library	PAIRED	GENOMIC	WGS	RANDOM	482	A59127	SRX2238879	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043506-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL043506-04A-01D A59127 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59127_3_lanes_dupsFlagged_reheadered.bam	SRR4415861	@dbgap@:reads/SRP011999/SRS1761171/SRX2238879/SRR4415861/SRR4415861.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043506-04A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043506.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL043506	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043506-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043506-04A-01D	DNA	EFO	SRS1761171	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043506-04A-01D A59127 library	PAIRED	GENOMIC	WGS	RANDOM	482	A59127	SRX2238879	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043506-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL043506-04A-01D A59127 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59127_3_lanes_dupsFlagged_reheadered.bam	SRR4415861	@dbgap@:reads/SRP011999/SRS1761171/SRX2238879/SRR4415861/SRR4415861.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043506-04A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043506.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL043506	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043506-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043506-04A-01D	DNA	EFO	SRS1761171	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043506-04A-01D A59127 library	PAIRED	GENOMIC	WGS	RANDOM	482	A59127	SRX2238879	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043506-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL043506-04A-01D A59127 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59127_3_lanes_dupsFlagged_reheadered.bam	SRR4415861	@dbgap@:reads/SRP011999/SRS1761171/SRX2238879/SRR4415861/SRR4415861.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043506-04A-01D.indel.vcf	3						
TARGET-15-SJMPAL043506	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043506-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043506-04A-01D	DNA	EFO	SRS1761171	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043506-04A-01D A59127 library	PAIRED	GENOMIC	WGS	RANDOM	482	A59127	SRX2238879	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043506-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL043506-04A-01D A59127 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59127_3_lanes_dupsFlagged_reheadered.bam	SRR4415861	@dbgap@:reads/SRP011999/SRS1761171/SRX2238879/SRR4415861/SRR4415861.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043506.quality_tagged.vcf	3						
TARGET-15-SJMPAL043506	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043506-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043506-04A-01D	DNA	EFO	SRS1761171	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043506-04A-01D A59127 library	PAIRED	GENOMIC	WGS	RANDOM	482	A59127	SRX2238879	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043506-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL043506-04A-01D A59127 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59127_3_lanes_dupsFlagged_reheadered.bam	SRR4415861	@dbgap@:reads/SRP011999/SRS1761171/SRX2238879/SRR4415861/SRR4415861.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043506-04A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043506-04A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043506	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043506-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043506-04A-01D	DNA	EFO	SRS1761171	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043506-04A-01D A59127 library	PAIRED	GENOMIC	WGS	RANDOM	482	A59127	SRX2238879	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043506-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL043506-04A-01D A59127 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59127_3_lanes_dupsFlagged_reheadered.bam	SRR4415861	@dbgap@:reads/SRP011999/SRS1761171/SRX2238879/SRR4415861/SRR4415861.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043506.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043506	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043506-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043506-04A-01D	DNA	EFO	SRS1761171	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043506-04A-01D A59127 library	PAIRED	GENOMIC	WGS	RANDOM	482	A59127	SRX2238879	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043506-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL043506-04A-01D A59127 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59127_3_lanes_dupsFlagged_reheadered.bam	SRR4415861	@dbgap@:reads/SRP011999/SRS1761171/SRX2238879/SRR4415861/SRR4415861.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043506-04A-01D_TARGET-15-SJMPAL043506-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043506-04A-01D_TARGET-15-SJMPAL043506-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043506	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043506-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043506-04A-01D	DNA	EFO	SRS1761171	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043506-04A-01D A59127 library	PAIRED	GENOMIC	WGS	RANDOM	482	A59127	SRX2238879	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043506-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-22	TARGET-15-SJMPAL043506-04A-01D A59127 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59127_3_lanes_dupsFlagged_reheadered.bam	SRR4415861	@dbgap@:reads/SRP011999/SRS1761171/SRX2238879/SRR4415861/SRR4415861.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043506-04A-01D_TARGET-15-SJMPAL043506-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043506-04A-01D_TARGET-15-SJMPAL043506-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043506.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043506	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043506-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043506-14A.1-01D	DNA	EFO	SRS1761168	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043506-14A.1-01D A59237 library	PAIRED	GENOMIC	WGS	RANDOM	446	A59237	SRX2238876	"WGS analysis of normal sample TARGET-15-SJMPAL043506-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043506-14A.1-01D A59237 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59237_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634879	@dbgap@:reads/SRP011999/SRS1761168/SRX2238876/SRR5634879/SRR5634879.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043506.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043506	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043506-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043506-14A.1-01D	DNA	EFO	SRS1761168	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043506-14A.1-01D A59237 library	PAIRED	GENOMIC	WGS	RANDOM	446	A59237	SRX2238876	"WGS analysis of normal sample TARGET-15-SJMPAL043506-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043506-14A.1-01D A59237 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59237_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634879	@dbgap@:reads/SRP011999/SRS1761168/SRX2238876/SRR5634879/SRR5634879.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043506.quality_tagged.vcf	3						
TARGET-15-SJMPAL043506	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043506-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043506-14A.1-01D	DNA	EFO	SRS1761168	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043506-14A.1-01D A59237 library	PAIRED	GENOMIC	WGS	RANDOM	446	A59237	SRX2238876	"WGS analysis of normal sample TARGET-15-SJMPAL043506-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043506-14A.1-01D A59237 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59237_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634879	@dbgap@:reads/SRP011999/SRS1761168/SRX2238876/SRR5634879/SRR5634879.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043506-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043506-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043506	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043506-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043506-14A.1-01D	DNA	EFO	SRS1761168	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043506-14A.1-01D A59237 library	PAIRED	GENOMIC	WGS	RANDOM	446	A59237	SRX2238876	"WGS analysis of normal sample TARGET-15-SJMPAL043506-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043506-14A.1-01D A59237 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59237_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634879	@dbgap@:reads/SRP011999/SRS1761168/SRX2238876/SRR5634879/SRR5634879.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043506.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043506	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043506-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043506-14A.1-01D	DNA	EFO	SRS1761168	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043506-14A.1-01D A59237 library	PAIRED	GENOMIC	WGS	RANDOM	446	A59237	SRX2238876	"WGS analysis of normal sample TARGET-15-SJMPAL043506-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043506-14A.1-01D A59237 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59237_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634879	@dbgap@:reads/SRP011999/SRS1761168/SRX2238876/SRR5634879/SRR5634879.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043506-04A-01D_TARGET-15-SJMPAL043506-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043506-04A-01D_TARGET-15-SJMPAL043506-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043506	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043506-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043506-14A.1-01D	DNA	EFO	SRS1761168	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043506-14A.1-01D A59237 library	PAIRED	GENOMIC	WGS	RANDOM	446	A59237	SRX2238876	"WGS analysis of normal sample TARGET-15-SJMPAL043506-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043506-14A.1-01D A59237 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59237_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634879	@dbgap@:reads/SRP011999/SRS1761168/SRX2238876/SRR5634879/SRR5634879.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043506-04A-01D_TARGET-15-SJMPAL043506-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043506-04A-01D_TARGET-15-SJMPAL043506-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043506.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043507	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043507-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043507-04A-01D	DNA	EFO	SRS1761135	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043507-04A-01D A59131 library	PAIRED	GENOMIC	WGS	RANDOM	477	A59131	SRX2238843	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043507-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043507-04A-01D A59131 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59131_3_lanes_dupsFlagged_reheadered.bam	SRR4415923	@dbgap@:reads/SRP011999/SRS1761135/SRX2238843/SRR4415923/SRR4415923.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043507.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043507	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043507-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043507-04A-01D	DNA	EFO	SRS1761135	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043507-04A-01D A59131 library	PAIRED	GENOMIC	WGS	RANDOM	477	A59131	SRX2238843	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043507-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043507-04A-01D A59131 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59131_3_lanes_dupsFlagged_reheadered.bam	SRR4415923	@dbgap@:reads/SRP011999/SRS1761135/SRX2238843/SRR4415923/SRR4415923.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043507-04A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043507.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL043507	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043507-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043507-04A-01D	DNA	EFO	SRS1761135	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043507-04A-01D A59131 library	PAIRED	GENOMIC	WGS	RANDOM	477	A59131	SRX2238843	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043507-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043507-04A-01D A59131 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59131_3_lanes_dupsFlagged_reheadered.bam	SRR4415923	@dbgap@:reads/SRP011999/SRS1761135/SRX2238843/SRR4415923/SRR4415923.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043507-04A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043507.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL043507	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043507-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043507-04A-01D	DNA	EFO	SRS1761135	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043507-04A-01D A59131 library	PAIRED	GENOMIC	WGS	RANDOM	477	A59131	SRX2238843	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043507-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043507-04A-01D A59131 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59131_3_lanes_dupsFlagged_reheadered.bam	SRR4415923	@dbgap@:reads/SRP011999/SRS1761135/SRX2238843/SRR4415923/SRR4415923.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043507-04A-01D.indel.vcf	3						
TARGET-15-SJMPAL043507	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043507-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043507-04A-01D	DNA	EFO	SRS1761135	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043507-04A-01D A59131 library	PAIRED	GENOMIC	WGS	RANDOM	477	A59131	SRX2238843	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043507-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043507-04A-01D A59131 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59131_3_lanes_dupsFlagged_reheadered.bam	SRR4415923	@dbgap@:reads/SRP011999/SRS1761135/SRX2238843/SRR4415923/SRR4415923.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043507.quality_tagged.vcf	3						
TARGET-15-SJMPAL043507	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043507-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043507-04A-01D	DNA	EFO	SRS1761135	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043507-04A-01D A59131 library	PAIRED	GENOMIC	WGS	RANDOM	477	A59131	SRX2238843	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043507-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043507-04A-01D A59131 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59131_3_lanes_dupsFlagged_reheadered.bam	SRR4415923	@dbgap@:reads/SRP011999/SRS1761135/SRX2238843/SRR4415923/SRR4415923.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043507-04A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043507-04A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043507	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043507-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043507-04A-01D	DNA	EFO	SRS1761135	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043507-04A-01D A59131 library	PAIRED	GENOMIC	WGS	RANDOM	477	A59131	SRX2238843	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043507-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043507-04A-01D A59131 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59131_3_lanes_dupsFlagged_reheadered.bam	SRR4415923	@dbgap@:reads/SRP011999/SRS1761135/SRX2238843/SRR4415923/SRR4415923.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043507.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043507	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043507-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043507-04A-01D	DNA	EFO	SRS1761135	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043507-04A-01D A59131 library	PAIRED	GENOMIC	WGS	RANDOM	477	A59131	SRX2238843	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043507-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043507-04A-01D A59131 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59131_3_lanes_dupsFlagged_reheadered.bam	SRR4415923	@dbgap@:reads/SRP011999/SRS1761135/SRX2238843/SRR4415923/SRR4415923.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043507-04A-01D_TARGET-15-SJMPAL043507-15A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043507-04A-01D_TARGET-15-SJMPAL043507-15A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043507	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043507-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043507-04A-01D	DNA	EFO	SRS1761135	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043507-04A-01D A59131 library	PAIRED	GENOMIC	WGS	RANDOM	477	A59131	SRX2238843	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043507-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043507-04A-01D A59131 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59131_3_lanes_dupsFlagged_reheadered.bam	SRR4415923	@dbgap@:reads/SRP011999/SRS1761135/SRX2238843/SRR4415923/SRR4415923.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043507-04A-01D_TARGET-15-SJMPAL043507-15A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043507-04A-01D_TARGET-15-SJMPAL043507-15A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043507.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043507	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043507-15A	organism part	EFO	Bone Marrow	NCIt	"Fibroblasts from Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043507-15A-01D	DNA	EFO	SRS1761184	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043507-15A-01D A59240 library	PAIRED	GENOMIC	WGS	RANDOM	453	A59240	SRX2238893	"WGS analysis of normal sample TARGET-15-SJMPAL043507-15A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043507-15A-01D A59240 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59240_2_lanes_dupsFlagged_reheadered.bam	SRR4415858	@dbgap@:reads/SRP011999/SRS1761184/SRX2238893/SRR4415858/SRR4415858.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043507.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043507	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043507-15A	organism part	EFO	Bone Marrow	NCIt	"Fibroblasts from Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043507-15A-01D	DNA	EFO	SRS1761184	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043507-15A-01D A59240 library	PAIRED	GENOMIC	WGS	RANDOM	453	A59240	SRX2238893	"WGS analysis of normal sample TARGET-15-SJMPAL043507-15A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043507-15A-01D A59240 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59240_2_lanes_dupsFlagged_reheadered.bam	SRR4415858	@dbgap@:reads/SRP011999/SRS1761184/SRX2238893/SRR4415858/SRR4415858.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043507.quality_tagged.vcf	3						
TARGET-15-SJMPAL043507	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043507-15A	organism part	EFO	Bone Marrow	NCIt	"Fibroblasts from Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043507-15A-01D	DNA	EFO	SRS1761184	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043507-15A-01D A59240 library	PAIRED	GENOMIC	WGS	RANDOM	453	A59240	SRX2238893	"WGS analysis of normal sample TARGET-15-SJMPAL043507-15A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043507-15A-01D A59240 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59240_2_lanes_dupsFlagged_reheadered.bam	SRR4415858	@dbgap@:reads/SRP011999/SRS1761184/SRX2238893/SRR4415858/SRR4415858.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043507-15A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043507-15A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043507	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043507-15A	organism part	EFO	Bone Marrow	NCIt	"Fibroblasts from Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043507-15A-01D	DNA	EFO	SRS1761184	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043507-15A-01D A59240 library	PAIRED	GENOMIC	WGS	RANDOM	453	A59240	SRX2238893	"WGS analysis of normal sample TARGET-15-SJMPAL043507-15A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043507-15A-01D A59240 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59240_2_lanes_dupsFlagged_reheadered.bam	SRR4415858	@dbgap@:reads/SRP011999/SRS1761184/SRX2238893/SRR4415858/SRR4415858.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043507.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043507	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043507-15A	organism part	EFO	Bone Marrow	NCIt	"Fibroblasts from Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043507-15A-01D	DNA	EFO	SRS1761184	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043507-15A-01D A59240 library	PAIRED	GENOMIC	WGS	RANDOM	453	A59240	SRX2238893	"WGS analysis of normal sample TARGET-15-SJMPAL043507-15A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043507-15A-01D A59240 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59240_2_lanes_dupsFlagged_reheadered.bam	SRR4415858	@dbgap@:reads/SRP011999/SRS1761184/SRX2238893/SRR4415858/SRR4415858.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043507-04A-01D_TARGET-15-SJMPAL043507-15A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043507-04A-01D_TARGET-15-SJMPAL043507-15A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043507	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043507-15A	organism part	EFO	Bone Marrow	NCIt	"Fibroblasts from Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043507-15A-01D	DNA	EFO	SRS1761184	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043507-15A-01D A59240 library	PAIRED	GENOMIC	WGS	RANDOM	453	A59240	SRX2238893	"WGS analysis of normal sample TARGET-15-SJMPAL043507-15A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043507-15A-01D A59240 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59240_2_lanes_dupsFlagged_reheadered.bam	SRR4415858	@dbgap@:reads/SRP011999/SRS1761184/SRX2238893/SRR4415858/SRR4415858.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043507-04A-01D_TARGET-15-SJMPAL043507-15A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043507-04A-01D_TARGET-15-SJMPAL043507-15A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043507.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043508	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043508-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043508-09A-01D	DNA	EFO	SRS1761133	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043508-09A-01D A59132 library	PAIRED	GENOMIC	WGS	RANDOM	483	A59132	SRX2238841	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043508-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043508-09A-01D A59132 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59132_3_lanes_dupsFlagged_reheadered.bam	SRR4415841	@dbgap@:reads/SRP011999/SRS1761133/SRX2238841/SRR4415841/SRR4415841.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043508.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043508	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043508-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043508-09A-01D	DNA	EFO	SRS1761133	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043508-09A-01D A59132 library	PAIRED	GENOMIC	WGS	RANDOM	483	A59132	SRX2238841	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043508-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043508-09A-01D A59132 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59132_3_lanes_dupsFlagged_reheadered.bam	SRR4415841	@dbgap@:reads/SRP011999/SRS1761133/SRX2238841/SRR4415841/SRR4415841.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043508-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043508.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL043508	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043508-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043508-09A-01D	DNA	EFO	SRS1761133	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043508-09A-01D A59132 library	PAIRED	GENOMIC	WGS	RANDOM	483	A59132	SRX2238841	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043508-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043508-09A-01D A59132 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59132_3_lanes_dupsFlagged_reheadered.bam	SRR4415841	@dbgap@:reads/SRP011999/SRS1761133/SRX2238841/SRR4415841/SRR4415841.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043508-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043508.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL043508	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043508-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043508-09A-01D	DNA	EFO	SRS1761133	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043508-09A-01D A59132 library	PAIRED	GENOMIC	WGS	RANDOM	483	A59132	SRX2238841	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043508-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043508-09A-01D A59132 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59132_3_lanes_dupsFlagged_reheadered.bam	SRR4415841	@dbgap@:reads/SRP011999/SRS1761133/SRX2238841/SRR4415841/SRR4415841.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043508-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL043508	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043508-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043508-09A-01D	DNA	EFO	SRS1761133	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043508-09A-01D A59132 library	PAIRED	GENOMIC	WGS	RANDOM	483	A59132	SRX2238841	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043508-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043508-09A-01D A59132 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59132_3_lanes_dupsFlagged_reheadered.bam	SRR4415841	@dbgap@:reads/SRP011999/SRS1761133/SRX2238841/SRR4415841/SRR4415841.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043508.quality_tagged.vcf	3						
TARGET-15-SJMPAL043508	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043508-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043508-09A-01D	DNA	EFO	SRS1761133	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043508-09A-01D A59132 library	PAIRED	GENOMIC	WGS	RANDOM	483	A59132	SRX2238841	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043508-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043508-09A-01D A59132 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59132_3_lanes_dupsFlagged_reheadered.bam	SRR4415841	@dbgap@:reads/SRP011999/SRS1761133/SRX2238841/SRR4415841/SRR4415841.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043508-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043508-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043508	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043508-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043508-09A-01D	DNA	EFO	SRS1761133	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043508-09A-01D A59132 library	PAIRED	GENOMIC	WGS	RANDOM	483	A59132	SRX2238841	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043508-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043508-09A-01D A59132 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59132_3_lanes_dupsFlagged_reheadered.bam	SRR4415841	@dbgap@:reads/SRP011999/SRS1761133/SRX2238841/SRR4415841/SRR4415841.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043508.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043508	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043508-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043508-09A-01D	DNA	EFO	SRS1761133	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043508-09A-01D A59132 library	PAIRED	GENOMIC	WGS	RANDOM	483	A59132	SRX2238841	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043508-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043508-09A-01D A59132 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59132_3_lanes_dupsFlagged_reheadered.bam	SRR4415841	@dbgap@:reads/SRP011999/SRS1761133/SRX2238841/SRR4415841/SRR4415841.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043508-09A-01D_TARGET-15-SJMPAL043508-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043508-09A-01D_TARGET-15-SJMPAL043508-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043508	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043508-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043508-09A-01D	DNA	EFO	SRS1761133	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043508-09A-01D A59132 library	PAIRED	GENOMIC	WGS	RANDOM	483	A59132	SRX2238841	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043508-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043508-09A-01D A59132 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59132_3_lanes_dupsFlagged_reheadered.bam	SRR4415841	@dbgap@:reads/SRP011999/SRS1761133/SRX2238841/SRR4415841/SRR4415841.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043508-09A-01D_TARGET-15-SJMPAL043508-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043508-09A-01D_TARGET-15-SJMPAL043508-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043508.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043508	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043508-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043508-14A.1-01D	DNA	EFO	SRS1761192	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043508-14A.1-01D A59241 library	PAIRED	GENOMIC	WGS	RANDOM	440	A59241	SRX2238900	"WGS analysis of normal sample TARGET-15-SJMPAL043508-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043508-14A.1-01D A59241 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59241_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634870	@dbgap@:reads/SRP011999/SRS1761192/SRX2238900/SRR5634870/SRR5634870.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043508.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043508	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043508-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043508-14A.1-01D	DNA	EFO	SRS1761192	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043508-14A.1-01D A59241 library	PAIRED	GENOMIC	WGS	RANDOM	440	A59241	SRX2238900	"WGS analysis of normal sample TARGET-15-SJMPAL043508-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043508-14A.1-01D A59241 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59241_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634870	@dbgap@:reads/SRP011999/SRS1761192/SRX2238900/SRR5634870/SRR5634870.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043508.quality_tagged.vcf	3						
TARGET-15-SJMPAL043508	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043508-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043508-14A.1-01D	DNA	EFO	SRS1761192	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043508-14A.1-01D A59241 library	PAIRED	GENOMIC	WGS	RANDOM	440	A59241	SRX2238900	"WGS analysis of normal sample TARGET-15-SJMPAL043508-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043508-14A.1-01D A59241 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59241_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634870	@dbgap@:reads/SRP011999/SRS1761192/SRX2238900/SRR5634870/SRR5634870.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043508-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043508-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043508	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043508-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043508-14A.1-01D	DNA	EFO	SRS1761192	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043508-14A.1-01D A59241 library	PAIRED	GENOMIC	WGS	RANDOM	440	A59241	SRX2238900	"WGS analysis of normal sample TARGET-15-SJMPAL043508-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043508-14A.1-01D A59241 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59241_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634870	@dbgap@:reads/SRP011999/SRS1761192/SRX2238900/SRR5634870/SRR5634870.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043508.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043508	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043508-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043508-14A.1-01D	DNA	EFO	SRS1761192	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043508-14A.1-01D A59241 library	PAIRED	GENOMIC	WGS	RANDOM	440	A59241	SRX2238900	"WGS analysis of normal sample TARGET-15-SJMPAL043508-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043508-14A.1-01D A59241 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59241_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634870	@dbgap@:reads/SRP011999/SRS1761192/SRX2238900/SRR5634870/SRR5634870.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043508-09A-01D_TARGET-15-SJMPAL043508-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043508-09A-01D_TARGET-15-SJMPAL043508-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043508	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043508-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043508-14A.1-01D	DNA	EFO	SRS1761192	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043508-14A.1-01D A59241 library	PAIRED	GENOMIC	WGS	RANDOM	440	A59241	SRX2238900	"WGS analysis of normal sample TARGET-15-SJMPAL043508-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043508-14A.1-01D A59241 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59241_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634870	@dbgap@:reads/SRP011999/SRS1761192/SRX2238900/SRR5634870/SRR5634870.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043508-09A-01D_TARGET-15-SJMPAL043508-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043508-09A-01D_TARGET-15-SJMPAL043508-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043508.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043513	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043513-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043513-04A-01D	DNA	EFO	SRS1761193	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043513-04A-01D A59138 library	PAIRED	GENOMIC	WGS	RANDOM	492	A59138	SRX2238901	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043513-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043513-04A-01D A59138 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59138_3_lanes_dupsFlagged_reheadered.bam	SRR4415885	@dbgap@:reads/SRP011999/SRS1761193/SRX2238901/SRR4415885/SRR4415885.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043513.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043513	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043513-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043513-04A-01D	DNA	EFO	SRS1761193	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043513-04A-01D A59138 library	PAIRED	GENOMIC	WGS	RANDOM	492	A59138	SRX2238901	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043513-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043513-04A-01D A59138 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59138_3_lanes_dupsFlagged_reheadered.bam	SRR4415885	@dbgap@:reads/SRP011999/SRS1761193/SRX2238901/SRR4415885/SRR4415885.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043513-04A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043513.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL043513	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043513-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043513-04A-01D	DNA	EFO	SRS1761193	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043513-04A-01D A59138 library	PAIRED	GENOMIC	WGS	RANDOM	492	A59138	SRX2238901	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043513-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043513-04A-01D A59138 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59138_3_lanes_dupsFlagged_reheadered.bam	SRR4415885	@dbgap@:reads/SRP011999/SRS1761193/SRX2238901/SRR4415885/SRR4415885.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043513-04A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043513.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL043513	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043513-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043513-04A-01D	DNA	EFO	SRS1761193	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043513-04A-01D A59138 library	PAIRED	GENOMIC	WGS	RANDOM	492	A59138	SRX2238901	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043513-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043513-04A-01D A59138 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59138_3_lanes_dupsFlagged_reheadered.bam	SRR4415885	@dbgap@:reads/SRP011999/SRS1761193/SRX2238901/SRR4415885/SRR4415885.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043513-04A-01D.indel.vcf	3						
TARGET-15-SJMPAL043513	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043513-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043513-04A-01D	DNA	EFO	SRS1761193	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043513-04A-01D A59138 library	PAIRED	GENOMIC	WGS	RANDOM	492	A59138	SRX2238901	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043513-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043513-04A-01D A59138 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59138_3_lanes_dupsFlagged_reheadered.bam	SRR4415885	@dbgap@:reads/SRP011999/SRS1761193/SRX2238901/SRR4415885/SRR4415885.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043513.quality_tagged.vcf	3						
TARGET-15-SJMPAL043513	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043513-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043513-04A-01D	DNA	EFO	SRS1761193	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043513-04A-01D A59138 library	PAIRED	GENOMIC	WGS	RANDOM	492	A59138	SRX2238901	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043513-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043513-04A-01D A59138 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59138_3_lanes_dupsFlagged_reheadered.bam	SRR4415885	@dbgap@:reads/SRP011999/SRS1761193/SRX2238901/SRR4415885/SRR4415885.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043513-04A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043513-04A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043513	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043513-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043513-04A-01D	DNA	EFO	SRS1761193	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043513-04A-01D A59138 library	PAIRED	GENOMIC	WGS	RANDOM	492	A59138	SRX2238901	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043513-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043513-04A-01D A59138 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59138_3_lanes_dupsFlagged_reheadered.bam	SRR4415885	@dbgap@:reads/SRP011999/SRS1761193/SRX2238901/SRR4415885/SRR4415885.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043513.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043513	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043513-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043513-04A-01D	DNA	EFO	SRS1761193	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043513-04A-01D A59138 library	PAIRED	GENOMIC	WGS	RANDOM	492	A59138	SRX2238901	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043513-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043513-04A-01D A59138 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59138_3_lanes_dupsFlagged_reheadered.bam	SRR4415885	@dbgap@:reads/SRP011999/SRS1761193/SRX2238901/SRR4415885/SRR4415885.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043513-04A-01D_TARGET-15-SJMPAL043513-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043513-04A-01D_TARGET-15-SJMPAL043513-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043513	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043513-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043513-04A-01D	DNA	EFO	SRS1761193	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043513-04A-01D A59138 library	PAIRED	GENOMIC	WGS	RANDOM	492	A59138	SRX2238901	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043513-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043513-04A-01D A59138 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59138_3_lanes_dupsFlagged_reheadered.bam	SRR4415885	@dbgap@:reads/SRP011999/SRS1761193/SRX2238901/SRR4415885/SRR4415885.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043513-04A-01D_TARGET-15-SJMPAL043513-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043513-04A-01D_TARGET-15-SJMPAL043513-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043513.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043513	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043513-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043513-14A-01D	DNA	EFO	SRS1761175	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043513-14A-01D A59247 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59247	SRX2238883	"WGS analysis of normal sample TARGET-15-SJMPAL043513-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043513-14A-01D A59247 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59247_2_lanes_dupsFlagged_reheadered.bam	SRR4415910	@dbgap@:reads/SRP011999/SRS1761175/SRX2238883/SRR4415910/SRR4415910.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043513.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043513	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043513-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043513-14A-01D	DNA	EFO	SRS1761175	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043513-14A-01D A59247 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59247	SRX2238883	"WGS analysis of normal sample TARGET-15-SJMPAL043513-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043513-14A-01D A59247 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59247_2_lanes_dupsFlagged_reheadered.bam	SRR4415910	@dbgap@:reads/SRP011999/SRS1761175/SRX2238883/SRR4415910/SRR4415910.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043513.quality_tagged.vcf	3						
TARGET-15-SJMPAL043513	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043513-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043513-14A-01D	DNA	EFO	SRS1761175	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043513-14A-01D A59247 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59247	SRX2238883	"WGS analysis of normal sample TARGET-15-SJMPAL043513-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043513-14A-01D A59247 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59247_2_lanes_dupsFlagged_reheadered.bam	SRR4415910	@dbgap@:reads/SRP011999/SRS1761175/SRX2238883/SRR4415910/SRR4415910.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043513-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043513-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043513	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043513-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043513-14A-01D	DNA	EFO	SRS1761175	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043513-14A-01D A59247 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59247	SRX2238883	"WGS analysis of normal sample TARGET-15-SJMPAL043513-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043513-14A-01D A59247 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59247_2_lanes_dupsFlagged_reheadered.bam	SRR4415910	@dbgap@:reads/SRP011999/SRS1761175/SRX2238883/SRR4415910/SRR4415910.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043513.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043513	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043513-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043513-14A-01D	DNA	EFO	SRS1761175	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043513-14A-01D A59247 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59247	SRX2238883	"WGS analysis of normal sample TARGET-15-SJMPAL043513-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043513-14A-01D A59247 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59247_2_lanes_dupsFlagged_reheadered.bam	SRR4415910	@dbgap@:reads/SRP011999/SRS1761175/SRX2238883/SRR4415910/SRR4415910.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043513-04A-01D_TARGET-15-SJMPAL043513-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043513-04A-01D_TARGET-15-SJMPAL043513-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043513	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043513-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043513-14A-01D	DNA	EFO	SRS1761175	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043513-14A-01D A59247 library	PAIRED	GENOMIC	WGS	RANDOM	454	A59247	SRX2238883	"WGS analysis of normal sample TARGET-15-SJMPAL043513-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043513-14A-01D A59247 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59247_2_lanes_dupsFlagged_reheadered.bam	SRR4415910	@dbgap@:reads/SRP011999/SRS1761175/SRX2238883/SRR4415910/SRR4415910.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043513-04A-01D_TARGET-15-SJMPAL043513-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043513-04A-01D_TARGET-15-SJMPAL043513-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043513.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043767	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043767-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043767-09A.1-01D	DNA	EFO	SRS1761182	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043767-09A.1-01D A59134 library	PAIRED	GENOMIC	WGS	RANDOM	490	A59134	SRX2238890	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043767-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043767-09A.1-01D A59134 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59134_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634835	@dbgap@:reads/SRP011999/SRS1761182/SRX2238890/SRR5634835/SRR5634835.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043767.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043767	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043767-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043767-09A.1-01D	DNA	EFO	SRS1761182	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043767-09A.1-01D A59134 library	PAIRED	GENOMIC	WGS	RANDOM	490	A59134	SRX2238890	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043767-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043767-09A.1-01D A59134 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59134_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634835	@dbgap@:reads/SRP011999/SRS1761182/SRX2238890/SRR5634835/SRR5634835.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043767-09A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043767.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL043767	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043767-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043767-09A.1-01D	DNA	EFO	SRS1761182	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043767-09A.1-01D A59134 library	PAIRED	GENOMIC	WGS	RANDOM	490	A59134	SRX2238890	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043767-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043767-09A.1-01D A59134 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59134_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634835	@dbgap@:reads/SRP011999/SRS1761182/SRX2238890/SRR5634835/SRR5634835.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043767-09A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043767.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL043767	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043767-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043767-09A.1-01D	DNA	EFO	SRS1761182	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043767-09A.1-01D A59134 library	PAIRED	GENOMIC	WGS	RANDOM	490	A59134	SRX2238890	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043767-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043767-09A.1-01D A59134 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59134_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634835	@dbgap@:reads/SRP011999/SRS1761182/SRX2238890/SRR5634835/SRR5634835.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043767-09A.1-01D.indel.vcf	3						
TARGET-15-SJMPAL043767	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043767-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043767-09A.1-01D	DNA	EFO	SRS1761182	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043767-09A.1-01D A59134 library	PAIRED	GENOMIC	WGS	RANDOM	490	A59134	SRX2238890	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043767-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043767-09A.1-01D A59134 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59134_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634835	@dbgap@:reads/SRP011999/SRS1761182/SRX2238890/SRR5634835/SRR5634835.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043767.quality_tagged.vcf	3						
TARGET-15-SJMPAL043767	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043767-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043767-09A.1-01D	DNA	EFO	SRS1761182	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043767-09A.1-01D A59134 library	PAIRED	GENOMIC	WGS	RANDOM	490	A59134	SRX2238890	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043767-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043767-09A.1-01D A59134 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59134_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634835	@dbgap@:reads/SRP011999/SRS1761182/SRX2238890/SRR5634835/SRR5634835.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043767-09A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043767-09A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043767	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043767-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043767-09A.1-01D	DNA	EFO	SRS1761182	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043767-09A.1-01D A59134 library	PAIRED	GENOMIC	WGS	RANDOM	490	A59134	SRX2238890	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043767-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043767-09A.1-01D A59134 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59134_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634835	@dbgap@:reads/SRP011999/SRS1761182/SRX2238890/SRR5634835/SRR5634835.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043767.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043767	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043767-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043767-09A.1-01D	DNA	EFO	SRS1761182	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043767-09A.1-01D A59134 library	PAIRED	GENOMIC	WGS	RANDOM	490	A59134	SRX2238890	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043767-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043767-09A.1-01D A59134 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59134_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634835	@dbgap@:reads/SRP011999/SRS1761182/SRX2238890/SRR5634835/SRR5634835.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043767-09A.1-01D_TARGET-15-SJMPAL043767-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043767-09A.1-01D_TARGET-15-SJMPAL043767-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043767	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043767-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043767-09A.1-01D	DNA	EFO	SRS1761182	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043767-09A.1-01D A59134 library	PAIRED	GENOMIC	WGS	RANDOM	490	A59134	SRX2238890	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043767-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043767-09A.1-01D A59134 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59134_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634835	@dbgap@:reads/SRP011999/SRS1761182/SRX2238890/SRR5634835/SRR5634835.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043767-09A.1-01D_TARGET-15-SJMPAL043767-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043767-09A.1-01D_TARGET-15-SJMPAL043767-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043767.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043767	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043767-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043767-14A.1-01D	DNA	EFO	SRS1761132	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043767-14A.1-01D A59243 library	PAIRED	GENOMIC	WGS	RANDOM	424	A59243	SRX2238840	"WGS analysis of normal sample TARGET-15-SJMPAL043767-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043767-14A.1-01D A59243 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59243_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634861	@dbgap@:reads/SRP011999/SRS1761132/SRX2238840/SRR5634861/SRR5634861.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043767.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043767	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043767-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043767-14A.1-01D	DNA	EFO	SRS1761132	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043767-14A.1-01D A59243 library	PAIRED	GENOMIC	WGS	RANDOM	424	A59243	SRX2238840	"WGS analysis of normal sample TARGET-15-SJMPAL043767-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043767-14A.1-01D A59243 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59243_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634861	@dbgap@:reads/SRP011999/SRS1761132/SRX2238840/SRR5634861/SRR5634861.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043767.quality_tagged.vcf	3						
TARGET-15-SJMPAL043767	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043767-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043767-14A.1-01D	DNA	EFO	SRS1761132	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043767-14A.1-01D A59243 library	PAIRED	GENOMIC	WGS	RANDOM	424	A59243	SRX2238840	"WGS analysis of normal sample TARGET-15-SJMPAL043767-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043767-14A.1-01D A59243 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59243_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634861	@dbgap@:reads/SRP011999/SRS1761132/SRX2238840/SRR5634861/SRR5634861.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043767-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043767-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043767	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043767-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043767-14A.1-01D	DNA	EFO	SRS1761132	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043767-14A.1-01D A59243 library	PAIRED	GENOMIC	WGS	RANDOM	424	A59243	SRX2238840	"WGS analysis of normal sample TARGET-15-SJMPAL043767-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043767-14A.1-01D A59243 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59243_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634861	@dbgap@:reads/SRP011999/SRS1761132/SRX2238840/SRR5634861/SRR5634861.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043767.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043767	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043767-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043767-14A.1-01D	DNA	EFO	SRS1761132	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043767-14A.1-01D A59243 library	PAIRED	GENOMIC	WGS	RANDOM	424	A59243	SRX2238840	"WGS analysis of normal sample TARGET-15-SJMPAL043767-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043767-14A.1-01D A59243 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59243_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634861	@dbgap@:reads/SRP011999/SRS1761132/SRX2238840/SRR5634861/SRR5634861.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043767-09A.1-01D_TARGET-15-SJMPAL043767-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043767-09A.1-01D_TARGET-15-SJMPAL043767-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043767	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043767-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043767-14A.1-01D	DNA	EFO	SRS1761132	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043767-14A.1-01D A59243 library	PAIRED	GENOMIC	WGS	RANDOM	424	A59243	SRX2238840	"WGS analysis of normal sample TARGET-15-SJMPAL043767-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043767-14A.1-01D A59243 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59243_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634861	@dbgap@:reads/SRP011999/SRS1761132/SRX2238840/SRR5634861/SRR5634861.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043767-09A.1-01D_TARGET-15-SJMPAL043767-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043767-09A.1-01D_TARGET-15-SJMPAL043767-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043767.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043768	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043768-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043768-09A.1-01D	DNA	EFO	SRS1761143	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043768-09A.1-01D A59135 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59135	SRX2238851	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043768-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043768-09A.1-01D A59135 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59135_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634874	@dbgap@:reads/SRP011999/SRS1761143/SRX2238851/SRR5634874/SRR5634874.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043768.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043768	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043768-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043768-09A.1-01D	DNA	EFO	SRS1761143	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043768-09A.1-01D A59135 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59135	SRX2238851	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043768-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043768-09A.1-01D A59135 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59135_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634874	@dbgap@:reads/SRP011999/SRS1761143/SRX2238851/SRR5634874/SRR5634874.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043768-09A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043768.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL043768	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043768-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043768-09A.1-01D	DNA	EFO	SRS1761143	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043768-09A.1-01D A59135 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59135	SRX2238851	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043768-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043768-09A.1-01D A59135 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59135_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634874	@dbgap@:reads/SRP011999/SRS1761143/SRX2238851/SRR5634874/SRR5634874.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043768-09A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043768.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL043768	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043768-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043768-09A.1-01D	DNA	EFO	SRS1761143	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043768-09A.1-01D A59135 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59135	SRX2238851	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043768-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043768-09A.1-01D A59135 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59135_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634874	@dbgap@:reads/SRP011999/SRS1761143/SRX2238851/SRR5634874/SRR5634874.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043768-09A.1-01D.indel.vcf	3						
TARGET-15-SJMPAL043768	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043768-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043768-09A.1-01D	DNA	EFO	SRS1761143	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043768-09A.1-01D A59135 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59135	SRX2238851	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043768-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043768-09A.1-01D A59135 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59135_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634874	@dbgap@:reads/SRP011999/SRS1761143/SRX2238851/SRR5634874/SRR5634874.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043768.quality_tagged.vcf	3						
TARGET-15-SJMPAL043768	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043768-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043768-09A.1-01D	DNA	EFO	SRS1761143	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043768-09A.1-01D A59135 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59135	SRX2238851	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043768-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043768-09A.1-01D A59135 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59135_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634874	@dbgap@:reads/SRP011999/SRS1761143/SRX2238851/SRR5634874/SRR5634874.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043768-09A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043768-09A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043768	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043768-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043768-09A.1-01D	DNA	EFO	SRS1761143	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043768-09A.1-01D A59135 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59135	SRX2238851	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043768-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043768-09A.1-01D A59135 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59135_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634874	@dbgap@:reads/SRP011999/SRS1761143/SRX2238851/SRR5634874/SRR5634874.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043768.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043768	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043768-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043768-09A.1-01D	DNA	EFO	SRS1761143	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043768-09A.1-01D A59135 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59135	SRX2238851	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043768-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043768-09A.1-01D A59135 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59135_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634874	@dbgap@:reads/SRP011999/SRS1761143/SRX2238851/SRR5634874/SRR5634874.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043768-09A.1-01D_TARGET-15-SJMPAL043768-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043768-09A.1-01D_TARGET-15-SJMPAL043768-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043768	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043768-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043768-09A.1-01D	DNA	EFO	SRS1761143	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043768-09A.1-01D A59135 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59135	SRX2238851	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043768-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-04-25	TARGET-15-SJMPAL043768-09A.1-01D A59135 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59135_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634874	@dbgap@:reads/SRP011999/SRS1761143/SRX2238851/SRR5634874/SRR5634874.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043768-09A.1-01D_TARGET-15-SJMPAL043768-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043768-09A.1-01D_TARGET-15-SJMPAL043768-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043768.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043768	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043768-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043768-14A.1-01D	DNA	EFO	SRS1761107	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043768-14A.1-01D A59244 library	PAIRED	GENOMIC	WGS	RANDOM	422	A59244	SRX2238815	"WGS analysis of normal sample TARGET-15-SJMPAL043768-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043768-14A.1-01D A59244 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59244_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634866	@dbgap@:reads/SRP011999/SRS1761107/SRX2238815/SRR5634866/SRR5634866.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043768.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043768	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043768-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043768-14A.1-01D	DNA	EFO	SRS1761107	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043768-14A.1-01D A59244 library	PAIRED	GENOMIC	WGS	RANDOM	422	A59244	SRX2238815	"WGS analysis of normal sample TARGET-15-SJMPAL043768-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043768-14A.1-01D A59244 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59244_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634866	@dbgap@:reads/SRP011999/SRS1761107/SRX2238815/SRR5634866/SRR5634866.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043768.quality_tagged.vcf	3						
TARGET-15-SJMPAL043768	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043768-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043768-14A.1-01D	DNA	EFO	SRS1761107	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043768-14A.1-01D A59244 library	PAIRED	GENOMIC	WGS	RANDOM	422	A59244	SRX2238815	"WGS analysis of normal sample TARGET-15-SJMPAL043768-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043768-14A.1-01D A59244 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59244_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634866	@dbgap@:reads/SRP011999/SRS1761107/SRX2238815/SRR5634866/SRR5634866.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043768-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043768-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043768	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043768-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043768-14A.1-01D	DNA	EFO	SRS1761107	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043768-14A.1-01D A59244 library	PAIRED	GENOMIC	WGS	RANDOM	422	A59244	SRX2238815	"WGS analysis of normal sample TARGET-15-SJMPAL043768-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043768-14A.1-01D A59244 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59244_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634866	@dbgap@:reads/SRP011999/SRS1761107/SRX2238815/SRR5634866/SRR5634866.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043768.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043768	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043768-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043768-14A.1-01D	DNA	EFO	SRS1761107	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043768-14A.1-01D A59244 library	PAIRED	GENOMIC	WGS	RANDOM	422	A59244	SRX2238815	"WGS analysis of normal sample TARGET-15-SJMPAL043768-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043768-14A.1-01D A59244 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59244_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634866	@dbgap@:reads/SRP011999/SRS1761107/SRX2238815/SRR5634866/SRR5634866.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043768-09A.1-01D_TARGET-15-SJMPAL043768-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043768-09A.1-01D_TARGET-15-SJMPAL043768-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043768	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043768-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043768-14A.1-01D	DNA	EFO	SRS1761107	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043768-14A.1-01D A59244 library	PAIRED	GENOMIC	WGS	RANDOM	422	A59244	SRX2238815	"WGS analysis of normal sample TARGET-15-SJMPAL043768-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043768-14A.1-01D A59244 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59244_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634866	@dbgap@:reads/SRP011999/SRS1761107/SRX2238815/SRR5634866/SRR5634866.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043768-09A.1-01D_TARGET-15-SJMPAL043768-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043768-09A.1-01D_TARGET-15-SJMPAL043768-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043768.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043769	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043769-03A.1	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043769-03A.1-01D	DNA	EFO	SRS1761206	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043769-03A.1-01D A59136 library	PAIRED	GENOMIC	WGS	RANDOM	460	A59136	SRX2238913	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043769-03A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043769-03A.1-01D A59136 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59136_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634852	@dbgap@:reads/SRP011999/SRS1761206/SRX2238913/SRR5634852/SRR5634852.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043769.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043769	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043769-03A.1	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043769-03A.1-01D	DNA	EFO	SRS1761206	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043769-03A.1-01D A59136 library	PAIRED	GENOMIC	WGS	RANDOM	460	A59136	SRX2238913	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043769-03A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043769-03A.1-01D A59136 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59136_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634852	@dbgap@:reads/SRP011999/SRS1761206/SRX2238913/SRR5634852/SRR5634852.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043769-03A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043769.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL043769	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043769-03A.1	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043769-03A.1-01D	DNA	EFO	SRS1761206	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043769-03A.1-01D A59136 library	PAIRED	GENOMIC	WGS	RANDOM	460	A59136	SRX2238913	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043769-03A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043769-03A.1-01D A59136 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59136_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634852	@dbgap@:reads/SRP011999/SRS1761206/SRX2238913/SRR5634852/SRR5634852.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043769-03A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043769.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL043769	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043769-03A.1	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043769-03A.1-01D	DNA	EFO	SRS1761206	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043769-03A.1-01D A59136 library	PAIRED	GENOMIC	WGS	RANDOM	460	A59136	SRX2238913	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043769-03A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043769-03A.1-01D A59136 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59136_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634852	@dbgap@:reads/SRP011999/SRS1761206/SRX2238913/SRR5634852/SRR5634852.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043769-03A.1-01D.indel.vcf	3						
TARGET-15-SJMPAL043769	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043769-03A.1	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043769-03A.1-01D	DNA	EFO	SRS1761206	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043769-03A.1-01D A59136 library	PAIRED	GENOMIC	WGS	RANDOM	460	A59136	SRX2238913	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043769-03A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043769-03A.1-01D A59136 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59136_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634852	@dbgap@:reads/SRP011999/SRS1761206/SRX2238913/SRR5634852/SRR5634852.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043769.quality_tagged.vcf	3						
TARGET-15-SJMPAL043769	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043769-03A.1	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043769-03A.1-01D	DNA	EFO	SRS1761206	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043769-03A.1-01D A59136 library	PAIRED	GENOMIC	WGS	RANDOM	460	A59136	SRX2238913	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043769-03A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043769-03A.1-01D A59136 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59136_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634852	@dbgap@:reads/SRP011999/SRS1761206/SRX2238913/SRR5634852/SRR5634852.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043769-03A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043769-03A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043769	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043769-03A.1	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043769-03A.1-01D	DNA	EFO	SRS1761206	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043769-03A.1-01D A59136 library	PAIRED	GENOMIC	WGS	RANDOM	460	A59136	SRX2238913	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043769-03A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043769-03A.1-01D A59136 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59136_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634852	@dbgap@:reads/SRP011999/SRS1761206/SRX2238913/SRR5634852/SRR5634852.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043769.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043769	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043769-03A.1	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043769-03A.1-01D	DNA	EFO	SRS1761206	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043769-03A.1-01D A59136 library	PAIRED	GENOMIC	WGS	RANDOM	460	A59136	SRX2238913	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043769-03A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043769-03A.1-01D A59136 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59136_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634852	@dbgap@:reads/SRP011999/SRS1761206/SRX2238913/SRR5634852/SRR5634852.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043769-03A.1-01D_TARGET-15-SJMPAL043769-10A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043769-03A.1-01D_TARGET-15-SJMPAL043769-10A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043769	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043769-03A.1	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043769-03A.1-01D	DNA	EFO	SRS1761206	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043769-03A.1-01D A59136 library	PAIRED	GENOMIC	WGS	RANDOM	460	A59136	SRX2238913	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043769-03A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043769-03A.1-01D A59136 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59136_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634852	@dbgap@:reads/SRP011999/SRS1761206/SRX2238913/SRR5634852/SRR5634852.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043769-03A.1-01D_TARGET-15-SJMPAL043769-10A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043769-03A.1-01D_TARGET-15-SJMPAL043769-10A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043769.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043769	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043769-10A.1	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043769-10A.1-01D	DNA	EFO	SRS1761123	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043769-10A.1-01D A59245 library	PAIRED	GENOMIC	WGS	RANDOM	425	A59245	SRX2238831	"WGS analysis of normal sample TARGET-15-SJMPAL043769-10A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043769-10A.1-01D A59245 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59245_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634834	@dbgap@:reads/SRP011999/SRS1761123/SRX2238831/SRR5634834/SRR5634834.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043769.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043769	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043769-10A.1	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043769-10A.1-01D	DNA	EFO	SRS1761123	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043769-10A.1-01D A59245 library	PAIRED	GENOMIC	WGS	RANDOM	425	A59245	SRX2238831	"WGS analysis of normal sample TARGET-15-SJMPAL043769-10A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043769-10A.1-01D A59245 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59245_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634834	@dbgap@:reads/SRP011999/SRS1761123/SRX2238831/SRR5634834/SRR5634834.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043769.quality_tagged.vcf	3						
TARGET-15-SJMPAL043769	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043769-10A.1	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043769-10A.1-01D	DNA	EFO	SRS1761123	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043769-10A.1-01D A59245 library	PAIRED	GENOMIC	WGS	RANDOM	425	A59245	SRX2238831	"WGS analysis of normal sample TARGET-15-SJMPAL043769-10A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043769-10A.1-01D A59245 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59245_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634834	@dbgap@:reads/SRP011999/SRS1761123/SRX2238831/SRR5634834/SRR5634834.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043769-10A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043769-10A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043769	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043769-10A.1	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043769-10A.1-01D	DNA	EFO	SRS1761123	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043769-10A.1-01D A59245 library	PAIRED	GENOMIC	WGS	RANDOM	425	A59245	SRX2238831	"WGS analysis of normal sample TARGET-15-SJMPAL043769-10A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043769-10A.1-01D A59245 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59245_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634834	@dbgap@:reads/SRP011999/SRS1761123/SRX2238831/SRR5634834/SRR5634834.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043769.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043769	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043769-10A.1	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043769-10A.1-01D	DNA	EFO	SRS1761123	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043769-10A.1-01D A59245 library	PAIRED	GENOMIC	WGS	RANDOM	425	A59245	SRX2238831	"WGS analysis of normal sample TARGET-15-SJMPAL043769-10A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043769-10A.1-01D A59245 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59245_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634834	@dbgap@:reads/SRP011999/SRS1761123/SRX2238831/SRR5634834/SRR5634834.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043769-03A.1-01D_TARGET-15-SJMPAL043769-10A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043769-03A.1-01D_TARGET-15-SJMPAL043769-10A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043769	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043769-10A.1	organism part	EFO	Peripheral Blood	NCIt	"Blood Derived Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043769-10A.1-01D	DNA	EFO	SRS1761123	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043769-10A.1-01D A59245 library	PAIRED	GENOMIC	WGS	RANDOM	425	A59245	SRX2238831	"WGS analysis of normal sample TARGET-15-SJMPAL043769-10A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043769-10A.1-01D A59245 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59245_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634834	@dbgap@:reads/SRP011999/SRS1761123/SRX2238831/SRR5634834/SRR5634834.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043769-03A.1-01D_TARGET-15-SJMPAL043769-10A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043769-03A.1-01D_TARGET-15-SJMPAL043769-10A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043769.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043770	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043770-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043770-09A.1-01D	DNA	EFO	SRS1761154	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043770-09A.1-01D A59137 library	PAIRED	GENOMIC	WGS	RANDOM	469	A59137	SRX2238862	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043770-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043770-09A.1-01D A59137 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59137_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634860	@dbgap@:reads/SRP011999/SRS1761154/SRX2238862/SRR5634860/SRR5634860.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043770.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043770	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043770-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043770-09A.1-01D	DNA	EFO	SRS1761154	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043770-09A.1-01D A59137 library	PAIRED	GENOMIC	WGS	RANDOM	469	A59137	SRX2238862	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043770-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043770-09A.1-01D A59137 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59137_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634860	@dbgap@:reads/SRP011999/SRS1761154/SRX2238862/SRR5634860/SRR5634860.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043770-09A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043770.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL043770	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043770-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043770-09A.1-01D	DNA	EFO	SRS1761154	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043770-09A.1-01D A59137 library	PAIRED	GENOMIC	WGS	RANDOM	469	A59137	SRX2238862	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043770-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043770-09A.1-01D A59137 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59137_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634860	@dbgap@:reads/SRP011999/SRS1761154/SRX2238862/SRR5634860/SRR5634860.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043770-09A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043770.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL043770	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043770-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043770-09A.1-01D	DNA	EFO	SRS1761154	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043770-09A.1-01D A59137 library	PAIRED	GENOMIC	WGS	RANDOM	469	A59137	SRX2238862	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043770-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043770-09A.1-01D A59137 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59137_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634860	@dbgap@:reads/SRP011999/SRS1761154/SRX2238862/SRR5634860/SRR5634860.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043770-09A.1-01D.indel.vcf	3						
TARGET-15-SJMPAL043770	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043770-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043770-09A.1-01D	DNA	EFO	SRS1761154	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043770-09A.1-01D A59137 library	PAIRED	GENOMIC	WGS	RANDOM	469	A59137	SRX2238862	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043770-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043770-09A.1-01D A59137 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59137_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634860	@dbgap@:reads/SRP011999/SRS1761154/SRX2238862/SRR5634860/SRR5634860.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043770.quality_tagged.vcf	3						
TARGET-15-SJMPAL043770	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043770-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043770-09A.1-01D	DNA	EFO	SRS1761154	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043770-09A.1-01D A59137 library	PAIRED	GENOMIC	WGS	RANDOM	469	A59137	SRX2238862	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043770-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043770-09A.1-01D A59137 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59137_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634860	@dbgap@:reads/SRP011999/SRS1761154/SRX2238862/SRR5634860/SRR5634860.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043770-09A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043770-09A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043770	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043770-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043770-09A.1-01D	DNA	EFO	SRS1761154	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043770-09A.1-01D A59137 library	PAIRED	GENOMIC	WGS	RANDOM	469	A59137	SRX2238862	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043770-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043770-09A.1-01D A59137 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59137_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634860	@dbgap@:reads/SRP011999/SRS1761154/SRX2238862/SRR5634860/SRR5634860.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043770.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043770	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043770-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043770-09A.1-01D	DNA	EFO	SRS1761154	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043770-09A.1-01D A59137 library	PAIRED	GENOMIC	WGS	RANDOM	469	A59137	SRX2238862	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043770-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043770-09A.1-01D A59137 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59137_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634860	@dbgap@:reads/SRP011999/SRS1761154/SRX2238862/SRR5634860/SRR5634860.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043770-09A.1-01D_TARGET-15-SJMPAL043770-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043770-09A.1-01D_TARGET-15-SJMPAL043770-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043770	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043770-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043770-09A.1-01D	DNA	EFO	SRS1761154	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043770-09A.1-01D A59137 library	PAIRED	GENOMIC	WGS	RANDOM	469	A59137	SRX2238862	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043770-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043770-09A.1-01D A59137 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59137_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634860	@dbgap@:reads/SRP011999/SRS1761154/SRX2238862/SRR5634860/SRR5634860.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043770-09A.1-01D_TARGET-15-SJMPAL043770-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043770-09A.1-01D_TARGET-15-SJMPAL043770-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043770.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043770	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043770-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043770-14A.1-01D	DNA	EFO	SRS1761157	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043770-14A.1-01D A59246 library	PAIRED	GENOMIC	WGS	RANDOM	427	A59246	SRX2238865	"WGS analysis of normal sample TARGET-15-SJMPAL043770-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043770-14A.1-01D A59246 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59246_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634858	@dbgap@:reads/SRP011999/SRS1761157/SRX2238865/SRR5634858/SRR5634858.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043770.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043770	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043770-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043770-14A.1-01D	DNA	EFO	SRS1761157	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043770-14A.1-01D A59246 library	PAIRED	GENOMIC	WGS	RANDOM	427	A59246	SRX2238865	"WGS analysis of normal sample TARGET-15-SJMPAL043770-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043770-14A.1-01D A59246 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59246_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634858	@dbgap@:reads/SRP011999/SRS1761157/SRX2238865/SRR5634858/SRR5634858.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043770.quality_tagged.vcf	3						
TARGET-15-SJMPAL043770	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043770-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043770-14A.1-01D	DNA	EFO	SRS1761157	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043770-14A.1-01D A59246 library	PAIRED	GENOMIC	WGS	RANDOM	427	A59246	SRX2238865	"WGS analysis of normal sample TARGET-15-SJMPAL043770-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043770-14A.1-01D A59246 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59246_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634858	@dbgap@:reads/SRP011999/SRS1761157/SRX2238865/SRR5634858/SRR5634858.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043770-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043770-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043770	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043770-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043770-14A.1-01D	DNA	EFO	SRS1761157	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043770-14A.1-01D A59246 library	PAIRED	GENOMIC	WGS	RANDOM	427	A59246	SRX2238865	"WGS analysis of normal sample TARGET-15-SJMPAL043770-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043770-14A.1-01D A59246 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59246_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634858	@dbgap@:reads/SRP011999/SRS1761157/SRX2238865/SRR5634858/SRR5634858.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043770.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043770	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043770-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043770-14A.1-01D	DNA	EFO	SRS1761157	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043770-14A.1-01D A59246 library	PAIRED	GENOMIC	WGS	RANDOM	427	A59246	SRX2238865	"WGS analysis of normal sample TARGET-15-SJMPAL043770-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043770-14A.1-01D A59246 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59246_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634858	@dbgap@:reads/SRP011999/SRS1761157/SRX2238865/SRR5634858/SRR5634858.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043770-09A.1-01D_TARGET-15-SJMPAL043770-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043770-09A.1-01D_TARGET-15-SJMPAL043770-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043770	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043770-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043770-14A.1-01D	DNA	EFO	SRS1761157	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043770-14A.1-01D A59246 library	PAIRED	GENOMIC	WGS	RANDOM	427	A59246	SRX2238865	"WGS analysis of normal sample TARGET-15-SJMPAL043770-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-10	TARGET-15-SJMPAL043770-14A.1-01D A59246 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59246_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634858	@dbgap@:reads/SRP011999/SRS1761157/SRX2238865/SRR5634858/SRR5634858.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043770-09A.1-01D_TARGET-15-SJMPAL043770-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043770-09A.1-01D_TARGET-15-SJMPAL043770-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043770.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043771	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043771-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043771-09A-01D	DNA	EFO	SRS1761144	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043771-09A-01D A59139 library	PAIRED	GENOMIC	WGS	RANDOM	461	A59139	SRX2238852	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043771-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043771-09A-01D A59139 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59139_3_lanes_dupsFlagged_reheadered.bam	SRR4415883	@dbgap@:reads/SRP011999/SRS1761144/SRX2238852/SRR4415883/SRR4415883.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043771.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043771	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043771-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043771-09A-01D	DNA	EFO	SRS1761144	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043771-09A-01D A59139 library	PAIRED	GENOMIC	WGS	RANDOM	461	A59139	SRX2238852	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043771-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043771-09A-01D A59139 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59139_3_lanes_dupsFlagged_reheadered.bam	SRR4415883	@dbgap@:reads/SRP011999/SRS1761144/SRX2238852/SRR4415883/SRR4415883.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043771-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043771.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL043771	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043771-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043771-09A-01D	DNA	EFO	SRS1761144	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043771-09A-01D A59139 library	PAIRED	GENOMIC	WGS	RANDOM	461	A59139	SRX2238852	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043771-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043771-09A-01D A59139 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59139_3_lanes_dupsFlagged_reheadered.bam	SRR4415883	@dbgap@:reads/SRP011999/SRS1761144/SRX2238852/SRR4415883/SRR4415883.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043771-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043771.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL043771	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043771-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043771-09A-01D	DNA	EFO	SRS1761144	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043771-09A-01D A59139 library	PAIRED	GENOMIC	WGS	RANDOM	461	A59139	SRX2238852	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043771-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043771-09A-01D A59139 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59139_3_lanes_dupsFlagged_reheadered.bam	SRR4415883	@dbgap@:reads/SRP011999/SRS1761144/SRX2238852/SRR4415883/SRR4415883.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043771-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL043771	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043771-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043771-09A-01D	DNA	EFO	SRS1761144	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043771-09A-01D A59139 library	PAIRED	GENOMIC	WGS	RANDOM	461	A59139	SRX2238852	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043771-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043771-09A-01D A59139 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59139_3_lanes_dupsFlagged_reheadered.bam	SRR4415883	@dbgap@:reads/SRP011999/SRS1761144/SRX2238852/SRR4415883/SRR4415883.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043771.quality_tagged.vcf	3						
TARGET-15-SJMPAL043771	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043771-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043771-09A-01D	DNA	EFO	SRS1761144	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043771-09A-01D A59139 library	PAIRED	GENOMIC	WGS	RANDOM	461	A59139	SRX2238852	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043771-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043771-09A-01D A59139 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59139_3_lanes_dupsFlagged_reheadered.bam	SRR4415883	@dbgap@:reads/SRP011999/SRS1761144/SRX2238852/SRR4415883/SRR4415883.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043771-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043771-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043771	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043771-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043771-09A-01D	DNA	EFO	SRS1761144	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043771-09A-01D A59139 library	PAIRED	GENOMIC	WGS	RANDOM	461	A59139	SRX2238852	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043771-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043771-09A-01D A59139 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59139_3_lanes_dupsFlagged_reheadered.bam	SRR4415883	@dbgap@:reads/SRP011999/SRS1761144/SRX2238852/SRR4415883/SRR4415883.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043771.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043771	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043771-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043771-09A-01D	DNA	EFO	SRS1761144	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043771-09A-01D A59139 library	PAIRED	GENOMIC	WGS	RANDOM	461	A59139	SRX2238852	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043771-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043771-09A-01D A59139 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59139_3_lanes_dupsFlagged_reheadered.bam	SRR4415883	@dbgap@:reads/SRP011999/SRS1761144/SRX2238852/SRR4415883/SRR4415883.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043771-09A-01D_TARGET-15-SJMPAL043771-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043771-09A-01D_TARGET-15-SJMPAL043771-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043771	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043771-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043771-09A-01D	DNA	EFO	SRS1761144	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043771-09A-01D A59139 library	PAIRED	GENOMIC	WGS	RANDOM	461	A59139	SRX2238852	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043771-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043771-09A-01D A59139 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59139_3_lanes_dupsFlagged_reheadered.bam	SRR4415883	@dbgap@:reads/SRP011999/SRS1761144/SRX2238852/SRR4415883/SRR4415883.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043771-09A-01D_TARGET-15-SJMPAL043771-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043771-09A-01D_TARGET-15-SJMPAL043771-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043771.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043771	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043771-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043771-14A-01D	DNA	EFO	SRS1761145	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043771-14A-01D A59248 library	PAIRED	GENOMIC	WGS	RANDOM	449	A59248	SRX2238853	"WGS analysis of normal sample TARGET-15-SJMPAL043771-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043771-14A-01D A59248 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59248_2_lanes_dupsFlagged_reheadered.bam	SRR4415922	@dbgap@:reads/SRP011999/SRS1761145/SRX2238853/SRR4415922/SRR4415922.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043771.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043771	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043771-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043771-14A-01D	DNA	EFO	SRS1761145	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043771-14A-01D A59248 library	PAIRED	GENOMIC	WGS	RANDOM	449	A59248	SRX2238853	"WGS analysis of normal sample TARGET-15-SJMPAL043771-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043771-14A-01D A59248 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59248_2_lanes_dupsFlagged_reheadered.bam	SRR4415922	@dbgap@:reads/SRP011999/SRS1761145/SRX2238853/SRR4415922/SRR4415922.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043771.quality_tagged.vcf	3						
TARGET-15-SJMPAL043771	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043771-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043771-14A-01D	DNA	EFO	SRS1761145	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043771-14A-01D A59248 library	PAIRED	GENOMIC	WGS	RANDOM	449	A59248	SRX2238853	"WGS analysis of normal sample TARGET-15-SJMPAL043771-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043771-14A-01D A59248 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59248_2_lanes_dupsFlagged_reheadered.bam	SRR4415922	@dbgap@:reads/SRP011999/SRS1761145/SRX2238853/SRR4415922/SRR4415922.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043771-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043771-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043771	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043771-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043771-14A-01D	DNA	EFO	SRS1761145	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043771-14A-01D A59248 library	PAIRED	GENOMIC	WGS	RANDOM	449	A59248	SRX2238853	"WGS analysis of normal sample TARGET-15-SJMPAL043771-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043771-14A-01D A59248 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59248_2_lanes_dupsFlagged_reheadered.bam	SRR4415922	@dbgap@:reads/SRP011999/SRS1761145/SRX2238853/SRR4415922/SRR4415922.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043771.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043771	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043771-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043771-14A-01D	DNA	EFO	SRS1761145	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043771-14A-01D A59248 library	PAIRED	GENOMIC	WGS	RANDOM	449	A59248	SRX2238853	"WGS analysis of normal sample TARGET-15-SJMPAL043771-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043771-14A-01D A59248 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59248_2_lanes_dupsFlagged_reheadered.bam	SRR4415922	@dbgap@:reads/SRP011999/SRS1761145/SRX2238853/SRR4415922/SRR4415922.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043771-09A-01D_TARGET-15-SJMPAL043771-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043771-09A-01D_TARGET-15-SJMPAL043771-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043771	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043771-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043771-14A-01D	DNA	EFO	SRS1761145	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043771-14A-01D A59248 library	PAIRED	GENOMIC	WGS	RANDOM	449	A59248	SRX2238853	"WGS analysis of normal sample TARGET-15-SJMPAL043771-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043771-14A-01D A59248 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59248_2_lanes_dupsFlagged_reheadered.bam	SRR4415922	@dbgap@:reads/SRP011999/SRS1761145/SRX2238853/SRR4415922/SRR4415922.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043771-09A-01D_TARGET-15-SJMPAL043771-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043771-09A-01D_TARGET-15-SJMPAL043771-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043771.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043772	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043772-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043772-04A-01D	DNA	EFO	SRS1761174	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043772-04A-01D A59140 library	PAIRED	GENOMIC	WGS	RANDOM	481	A59140	SRX2238882	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043772-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043772-04A-01D A59140 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59140_3_lanes_dupsFlagged_reheadered.bam	SRR4415834	@dbgap@:reads/SRP011999/SRS1761174/SRX2238882/SRR4415834/SRR4415834.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043772.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043772	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043772-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043772-04A-01D	DNA	EFO	SRS1761174	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043772-04A-01D A59140 library	PAIRED	GENOMIC	WGS	RANDOM	481	A59140	SRX2238882	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043772-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043772-04A-01D A59140 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59140_3_lanes_dupsFlagged_reheadered.bam	SRR4415834	@dbgap@:reads/SRP011999/SRS1761174/SRX2238882/SRR4415834/SRR4415834.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043772-04A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043772.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL043772	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043772-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043772-04A-01D	DNA	EFO	SRS1761174	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043772-04A-01D A59140 library	PAIRED	GENOMIC	WGS	RANDOM	481	A59140	SRX2238882	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043772-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043772-04A-01D A59140 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59140_3_lanes_dupsFlagged_reheadered.bam	SRR4415834	@dbgap@:reads/SRP011999/SRS1761174/SRX2238882/SRR4415834/SRR4415834.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043772-04A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043772.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL043772	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043772-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043772-04A-01D	DNA	EFO	SRS1761174	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043772-04A-01D A59140 library	PAIRED	GENOMIC	WGS	RANDOM	481	A59140	SRX2238882	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043772-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043772-04A-01D A59140 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59140_3_lanes_dupsFlagged_reheadered.bam	SRR4415834	@dbgap@:reads/SRP011999/SRS1761174/SRX2238882/SRR4415834/SRR4415834.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043772-04A-01D.indel.vcf	3						
TARGET-15-SJMPAL043772	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043772-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043772-04A-01D	DNA	EFO	SRS1761174	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043772-04A-01D A59140 library	PAIRED	GENOMIC	WGS	RANDOM	481	A59140	SRX2238882	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043772-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043772-04A-01D A59140 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59140_3_lanes_dupsFlagged_reheadered.bam	SRR4415834	@dbgap@:reads/SRP011999/SRS1761174/SRX2238882/SRR4415834/SRR4415834.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043772.quality_tagged.vcf	3						
TARGET-15-SJMPAL043772	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043772-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043772-04A-01D	DNA	EFO	SRS1761174	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043772-04A-01D A59140 library	PAIRED	GENOMIC	WGS	RANDOM	481	A59140	SRX2238882	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043772-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043772-04A-01D A59140 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59140_3_lanes_dupsFlagged_reheadered.bam	SRR4415834	@dbgap@:reads/SRP011999/SRS1761174/SRX2238882/SRR4415834/SRR4415834.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043772-04A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043772-04A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043772	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043772-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043772-04A-01D	DNA	EFO	SRS1761174	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043772-04A-01D A59140 library	PAIRED	GENOMIC	WGS	RANDOM	481	A59140	SRX2238882	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043772-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043772-04A-01D A59140 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59140_3_lanes_dupsFlagged_reheadered.bam	SRR4415834	@dbgap@:reads/SRP011999/SRS1761174/SRX2238882/SRR4415834/SRR4415834.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043772.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043772	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043772-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043772-04A-01D	DNA	EFO	SRS1761174	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043772-04A-01D A59140 library	PAIRED	GENOMIC	WGS	RANDOM	481	A59140	SRX2238882	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043772-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043772-04A-01D A59140 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59140_3_lanes_dupsFlagged_reheadered.bam	SRR4415834	@dbgap@:reads/SRP011999/SRS1761174/SRX2238882/SRR4415834/SRR4415834.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043772-04A-01D_TARGET-15-SJMPAL043772-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043772-04A-01D_TARGET-15-SJMPAL043772-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043772	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Recurrent Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043772-04A	organism part	EFO	Bone Marrow	NCIt	"Recurrent Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043772-04A-01D	DNA	EFO	SRS1761174	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043772-04A-01D A59140 library	PAIRED	GENOMIC	WGS	RANDOM	481	A59140	SRX2238882	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043772-04A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043772-04A-01D A59140 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59140_3_lanes_dupsFlagged_reheadered.bam	SRR4415834	@dbgap@:reads/SRP011999/SRS1761174/SRX2238882/SRR4415834/SRR4415834.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043772-04A-01D_TARGET-15-SJMPAL043772-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043772-04A-01D_TARGET-15-SJMPAL043772-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043772.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043772	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043772-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043772-14A-01D	DNA	EFO	SRS1761159	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043772-14A-01D A59249 library	PAIRED	GENOMIC	WGS	RANDOM	440	A59249	SRX2238867	"WGS analysis of normal sample TARGET-15-SJMPAL043772-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043772-14A-01D A59249 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59249_2_lanes_dupsFlagged_reheadered.bam	SRR4415831	@dbgap@:reads/SRP011999/SRS1761159/SRX2238867/SRR4415831/SRR4415831.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043772.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043772	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043772-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043772-14A-01D	DNA	EFO	SRS1761159	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043772-14A-01D A59249 library	PAIRED	GENOMIC	WGS	RANDOM	440	A59249	SRX2238867	"WGS analysis of normal sample TARGET-15-SJMPAL043772-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043772-14A-01D A59249 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59249_2_lanes_dupsFlagged_reheadered.bam	SRR4415831	@dbgap@:reads/SRP011999/SRS1761159/SRX2238867/SRR4415831/SRR4415831.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043772.quality_tagged.vcf	3						
TARGET-15-SJMPAL043772	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043772-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043772-14A-01D	DNA	EFO	SRS1761159	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043772-14A-01D A59249 library	PAIRED	GENOMIC	WGS	RANDOM	440	A59249	SRX2238867	"WGS analysis of normal sample TARGET-15-SJMPAL043772-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043772-14A-01D A59249 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59249_2_lanes_dupsFlagged_reheadered.bam	SRR4415831	@dbgap@:reads/SRP011999/SRS1761159/SRX2238867/SRR4415831/SRR4415831.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043772-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043772-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043772	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043772-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043772-14A-01D	DNA	EFO	SRS1761159	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043772-14A-01D A59249 library	PAIRED	GENOMIC	WGS	RANDOM	440	A59249	SRX2238867	"WGS analysis of normal sample TARGET-15-SJMPAL043772-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043772-14A-01D A59249 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59249_2_lanes_dupsFlagged_reheadered.bam	SRR4415831	@dbgap@:reads/SRP011999/SRS1761159/SRX2238867/SRR4415831/SRR4415831.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043772.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043772	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043772-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043772-14A-01D	DNA	EFO	SRS1761159	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043772-14A-01D A59249 library	PAIRED	GENOMIC	WGS	RANDOM	440	A59249	SRX2238867	"WGS analysis of normal sample TARGET-15-SJMPAL043772-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043772-14A-01D A59249 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59249_2_lanes_dupsFlagged_reheadered.bam	SRR4415831	@dbgap@:reads/SRP011999/SRS1761159/SRX2238867/SRR4415831/SRR4415831.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043772-04A-01D_TARGET-15-SJMPAL043772-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043772-04A-01D_TARGET-15-SJMPAL043772-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043772	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043772-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043772-14A-01D	DNA	EFO	SRS1761159	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043772-14A-01D A59249 library	PAIRED	GENOMIC	WGS	RANDOM	440	A59249	SRX2238867	"WGS analysis of normal sample TARGET-15-SJMPAL043772-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043772-14A-01D A59249 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59249_2_lanes_dupsFlagged_reheadered.bam	SRR4415831	@dbgap@:reads/SRP011999/SRS1761159/SRX2238867/SRR4415831/SRR4415831.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043772-04A-01D_TARGET-15-SJMPAL043772-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043772-04A-01D_TARGET-15-SJMPAL043772-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043772.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043773	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043773-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043773-03A-01D	DNA	EFO	SRS1761120	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043773-03A-01D A59141 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59141	SRX2238828	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043773-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043773-03A-01D A59141 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59141_3_lanes_dupsFlagged_reheadered.bam	SRR4415860	@dbgap@:reads/SRP011999/SRS1761120/SRX2238828/SRR4415860/SRR4415860.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043773.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043773	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043773-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043773-03A-01D	DNA	EFO	SRS1761120	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043773-03A-01D A59141 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59141	SRX2238828	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043773-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043773-03A-01D A59141 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59141_3_lanes_dupsFlagged_reheadered.bam	SRR4415860	@dbgap@:reads/SRP011999/SRS1761120/SRX2238828/SRR4415860/SRR4415860.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043773-03A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043773.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL043773	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043773-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043773-03A-01D	DNA	EFO	SRS1761120	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043773-03A-01D A59141 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59141	SRX2238828	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043773-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043773-03A-01D A59141 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59141_3_lanes_dupsFlagged_reheadered.bam	SRR4415860	@dbgap@:reads/SRP011999/SRS1761120/SRX2238828/SRR4415860/SRR4415860.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043773-03A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043773.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL043773	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043773-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043773-03A-01D	DNA	EFO	SRS1761120	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043773-03A-01D A59141 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59141	SRX2238828	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043773-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043773-03A-01D A59141 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59141_3_lanes_dupsFlagged_reheadered.bam	SRR4415860	@dbgap@:reads/SRP011999/SRS1761120/SRX2238828/SRR4415860/SRR4415860.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043773-03A-01D.indel.vcf	3						
TARGET-15-SJMPAL043773	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043773-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043773-03A-01D	DNA	EFO	SRS1761120	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043773-03A-01D A59141 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59141	SRX2238828	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043773-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043773-03A-01D A59141 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59141_3_lanes_dupsFlagged_reheadered.bam	SRR4415860	@dbgap@:reads/SRP011999/SRS1761120/SRX2238828/SRR4415860/SRR4415860.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043773.quality_tagged.vcf	3						
TARGET-15-SJMPAL043773	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043773-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043773-03A-01D	DNA	EFO	SRS1761120	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043773-03A-01D A59141 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59141	SRX2238828	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043773-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043773-03A-01D A59141 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59141_3_lanes_dupsFlagged_reheadered.bam	SRR4415860	@dbgap@:reads/SRP011999/SRS1761120/SRX2238828/SRR4415860/SRR4415860.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043773-03A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043773-03A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043773	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043773-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043773-03A-01D	DNA	EFO	SRS1761120	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043773-03A-01D A59141 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59141	SRX2238828	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043773-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043773-03A-01D A59141 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59141_3_lanes_dupsFlagged_reheadered.bam	SRR4415860	@dbgap@:reads/SRP011999/SRS1761120/SRX2238828/SRR4415860/SRR4415860.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043773.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043773	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043773-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043773-03A-01D	DNA	EFO	SRS1761120	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043773-03A-01D A59141 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59141	SRX2238828	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043773-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043773-03A-01D A59141 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59141_3_lanes_dupsFlagged_reheadered.bam	SRR4415860	@dbgap@:reads/SRP011999/SRS1761120/SRX2238828/SRR4415860/SRR4415860.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043773-03A-01D_TARGET-15-SJMPAL043773-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043773-03A-01D_TARGET-15-SJMPAL043773-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043773	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043773-03A	organism part	EFO	Peripheral Blood	NCIt	"Primary Blood Derived Cancer - Peripheral Blood"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043773-03A-01D	DNA	EFO	SRS1761120	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043773-03A-01D A59141 library	PAIRED	GENOMIC	WGS	RANDOM	484	A59141	SRX2238828	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043773-03A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043773-03A-01D A59141 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59141_3_lanes_dupsFlagged_reheadered.bam	SRR4415860	@dbgap@:reads/SRP011999/SRS1761120/SRX2238828/SRR4415860/SRR4415860.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043773-03A-01D_TARGET-15-SJMPAL043773-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043773-03A-01D_TARGET-15-SJMPAL043773-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043773.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043773	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043773-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043773-14A-01D	DNA	EFO	SRS1761160	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043773-14A-01D A59250 library	PAIRED	GENOMIC	WGS	RANDOM	436	A59250	SRX2238868	"WGS analysis of normal sample TARGET-15-SJMPAL043773-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043773-14A-01D A59250 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59250_2_lanes_dupsFlagged_reheadered.bam	SRR4415880	@dbgap@:reads/SRP011999/SRS1761160/SRX2238868/SRR4415880/SRR4415880.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043773.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043773	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043773-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043773-14A-01D	DNA	EFO	SRS1761160	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043773-14A-01D A59250 library	PAIRED	GENOMIC	WGS	RANDOM	436	A59250	SRX2238868	"WGS analysis of normal sample TARGET-15-SJMPAL043773-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043773-14A-01D A59250 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59250_2_lanes_dupsFlagged_reheadered.bam	SRR4415880	@dbgap@:reads/SRP011999/SRS1761160/SRX2238868/SRR4415880/SRR4415880.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043773.quality_tagged.vcf	3						
TARGET-15-SJMPAL043773	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043773-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043773-14A-01D	DNA	EFO	SRS1761160	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043773-14A-01D A59250 library	PAIRED	GENOMIC	WGS	RANDOM	436	A59250	SRX2238868	"WGS analysis of normal sample TARGET-15-SJMPAL043773-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043773-14A-01D A59250 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59250_2_lanes_dupsFlagged_reheadered.bam	SRR4415880	@dbgap@:reads/SRP011999/SRS1761160/SRX2238868/SRR4415880/SRR4415880.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043773-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043773-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043773	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043773-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043773-14A-01D	DNA	EFO	SRS1761160	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043773-14A-01D A59250 library	PAIRED	GENOMIC	WGS	RANDOM	436	A59250	SRX2238868	"WGS analysis of normal sample TARGET-15-SJMPAL043773-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043773-14A-01D A59250 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59250_2_lanes_dupsFlagged_reheadered.bam	SRR4415880	@dbgap@:reads/SRP011999/SRS1761160/SRX2238868/SRR4415880/SRR4415880.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043773.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043773	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043773-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043773-14A-01D	DNA	EFO	SRS1761160	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043773-14A-01D A59250 library	PAIRED	GENOMIC	WGS	RANDOM	436	A59250	SRX2238868	"WGS analysis of normal sample TARGET-15-SJMPAL043773-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043773-14A-01D A59250 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59250_2_lanes_dupsFlagged_reheadered.bam	SRR4415880	@dbgap@:reads/SRP011999/SRS1761160/SRX2238868/SRR4415880/SRR4415880.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043773-03A-01D_TARGET-15-SJMPAL043773-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043773-03A-01D_TARGET-15-SJMPAL043773-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043773	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043773-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043773-14A-01D	DNA	EFO	SRS1761160	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043773-14A-01D A59250 library	PAIRED	GENOMIC	WGS	RANDOM	436	A59250	SRX2238868	"WGS analysis of normal sample TARGET-15-SJMPAL043773-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043773-14A-01D A59250 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59250_2_lanes_dupsFlagged_reheadered.bam	SRR4415880	@dbgap@:reads/SRP011999/SRS1761160/SRX2238868/SRR4415880/SRR4415880.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043773-03A-01D_TARGET-15-SJMPAL043773-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043773-03A-01D_TARGET-15-SJMPAL043773-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043773.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043774	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043774-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043774-09A.1-01D	DNA	EFO	SRS1761163	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043774-09A.1-01D A59142 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59142	SRX2238871	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043774-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043774-09A.1-01D A59142 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59142_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634842	@dbgap@:reads/SRP011999/SRS1761163/SRX2238871/SRR5634842/SRR5634842.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043774.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043774	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043774-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043774-09A.1-01D	DNA	EFO	SRS1761163	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043774-09A.1-01D A59142 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59142	SRX2238871	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043774-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043774-09A.1-01D A59142 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59142_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634842	@dbgap@:reads/SRP011999/SRS1761163/SRX2238871/SRR5634842/SRR5634842.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043774-09A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043774.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL043774	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043774-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043774-09A.1-01D	DNA	EFO	SRS1761163	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043774-09A.1-01D A59142 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59142	SRX2238871	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043774-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043774-09A.1-01D A59142 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59142_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634842	@dbgap@:reads/SRP011999/SRS1761163/SRX2238871/SRR5634842/SRR5634842.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043774-09A.1-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043774.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL043774	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043774-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043774-09A.1-01D	DNA	EFO	SRS1761163	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043774-09A.1-01D A59142 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59142	SRX2238871	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043774-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043774-09A.1-01D A59142 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59142_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634842	@dbgap@:reads/SRP011999/SRS1761163/SRX2238871/SRR5634842/SRR5634842.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043774-09A.1-01D.indel.vcf	3						
TARGET-15-SJMPAL043774	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043774-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043774-09A.1-01D	DNA	EFO	SRS1761163	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043774-09A.1-01D A59142 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59142	SRX2238871	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043774-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043774-09A.1-01D A59142 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59142_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634842	@dbgap@:reads/SRP011999/SRS1761163/SRX2238871/SRR5634842/SRR5634842.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043774.quality_tagged.vcf	3						
TARGET-15-SJMPAL043774	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043774-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043774-09A.1-01D	DNA	EFO	SRS1761163	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043774-09A.1-01D A59142 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59142	SRX2238871	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043774-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043774-09A.1-01D A59142 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59142_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634842	@dbgap@:reads/SRP011999/SRS1761163/SRX2238871/SRR5634842/SRR5634842.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043774-09A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043774-09A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043774	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043774-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043774-09A.1-01D	DNA	EFO	SRS1761163	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043774-09A.1-01D A59142 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59142	SRX2238871	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043774-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043774-09A.1-01D A59142 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59142_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634842	@dbgap@:reads/SRP011999/SRS1761163/SRX2238871/SRR5634842/SRR5634842.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043774.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043774	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043774-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043774-09A.1-01D	DNA	EFO	SRS1761163	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043774-09A.1-01D A59142 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59142	SRX2238871	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043774-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043774-09A.1-01D A59142 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59142_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634842	@dbgap@:reads/SRP011999/SRS1761163/SRX2238871/SRR5634842/SRR5634842.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043774-09A.1-01D_TARGET-15-SJMPAL043774-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043774-09A.1-01D_TARGET-15-SJMPAL043774-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043774	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043774-09A.1	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043774-09A.1-01D	DNA	EFO	SRS1761163	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043774-09A.1-01D A59142 library	PAIRED	GENOMIC	WGS	RANDOM	474	A59142	SRX2238871	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043774-09A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-02	TARGET-15-SJMPAL043774-09A.1-01D A59142 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59142_3_lanes_dupsFlagged_reheadered_2.bam	SRR5634842	@dbgap@:reads/SRP011999/SRS1761163/SRX2238871/SRR5634842/SRR5634842.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043774-09A.1-01D_TARGET-15-SJMPAL043774-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043774-09A.1-01D_TARGET-15-SJMPAL043774-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043774.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043774	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043774-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043774-14A.1-01D	DNA	EFO	SRS1761134	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043774-14A.1-01D A59251 library	PAIRED	GENOMIC	WGS	RANDOM	414	A59251	SRX2238842	"WGS analysis of normal sample TARGET-15-SJMPAL043774-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043774-14A.1-01D A59251 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59251_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634847	@dbgap@:reads/SRP011999/SRS1761134/SRX2238842/SRR5634847/SRR5634847.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043774.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043774	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043774-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043774-14A.1-01D	DNA	EFO	SRS1761134	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043774-14A.1-01D A59251 library	PAIRED	GENOMIC	WGS	RANDOM	414	A59251	SRX2238842	"WGS analysis of normal sample TARGET-15-SJMPAL043774-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043774-14A.1-01D A59251 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59251_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634847	@dbgap@:reads/SRP011999/SRS1761134/SRX2238842/SRR5634847/SRR5634847.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043774.quality_tagged.vcf	3						
TARGET-15-SJMPAL043774	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043774-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043774-14A.1-01D	DNA	EFO	SRS1761134	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043774-14A.1-01D A59251 library	PAIRED	GENOMIC	WGS	RANDOM	414	A59251	SRX2238842	"WGS analysis of normal sample TARGET-15-SJMPAL043774-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043774-14A.1-01D A59251 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59251_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634847	@dbgap@:reads/SRP011999/SRS1761134/SRX2238842/SRR5634847/SRR5634847.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043774-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043774-14A.1-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043774	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043774-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043774-14A.1-01D	DNA	EFO	SRS1761134	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043774-14A.1-01D A59251 library	PAIRED	GENOMIC	WGS	RANDOM	414	A59251	SRX2238842	"WGS analysis of normal sample TARGET-15-SJMPAL043774-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043774-14A.1-01D A59251 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59251_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634847	@dbgap@:reads/SRP011999/SRS1761134/SRX2238842/SRR5634847/SRR5634847.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043774.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043774	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043774-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043774-14A.1-01D	DNA	EFO	SRS1761134	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043774-14A.1-01D A59251 library	PAIRED	GENOMIC	WGS	RANDOM	414	A59251	SRX2238842	"WGS analysis of normal sample TARGET-15-SJMPAL043774-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043774-14A.1-01D A59251 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59251_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634847	@dbgap@:reads/SRP011999/SRS1761134/SRX2238842/SRR5634847/SRR5634847.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043774-09A.1-01D_TARGET-15-SJMPAL043774-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043774-09A.1-01D_TARGET-15-SJMPAL043774-14A.1-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043774	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043774-14A.1	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043774-14A.1-01D	DNA	EFO	SRS1761134	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043774-14A.1-01D A59251 library	PAIRED	GENOMIC	WGS	RANDOM	414	A59251	SRX2238842	"WGS analysis of normal sample TARGET-15-SJMPAL043774-14A.1-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043774-14A.1-01D A59251 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59251_2_lanes_dupsFlagged_reheadered_2.bam	SRR5634847	@dbgap@:reads/SRP011999/SRS1761134/SRX2238842/SRR5634847/SRR5634847.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043774-09A.1-01D_TARGET-15-SJMPAL043774-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043774-09A.1-01D_TARGET-15-SJMPAL043774-14A.1-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043774.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043775	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043775-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043775-09A-01D	DNA	EFO	SRS1761142	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043775-09A-01D A59143 library	PAIRED	GENOMIC	WGS	RANDOM	443	A59143	SRX2238850	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043775-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043775-09A-01D A59143 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59143_3_lanes_dupsFlagged_reheadered.bam	SRR4415906	@dbgap@:reads/SRP011999/SRS1761142/SRX2238850/SRR4415906/SRR4415906.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043775.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043775	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043775-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043775-09A-01D	DNA	EFO	SRS1761142	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043775-09A-01D A59143 library	PAIRED	GENOMIC	WGS	RANDOM	443	A59143	SRX2238850	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043775-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043775-09A-01D A59143 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59143_3_lanes_dupsFlagged_reheadered.bam	SRR4415906	@dbgap@:reads/SRP011999/SRS1761142/SRX2238850/SRR4415906/SRR4415906.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043775-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043775.gv2.genome.fusions.somatic.large.summary.tsv	3			
TARGET-15-SJMPAL043775	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043775-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043775-09A-01D	DNA	EFO	SRS1761142	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043775-09A-01D A59143 library	PAIRED	GENOMIC	WGS	RANDOM	443	A59143	SRX2238850	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043775-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043775-09A-01D A59143 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59143_3_lanes_dupsFlagged_reheadered.bam	SRR4415906	@dbgap@:reads/SRP011999/SRS1761142/SRX2238850/SRR4415906/SRR4415906.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043775-09A-01D.fusion.vcf	3	bcgsc.ca:Protocol:WGS-StructVariant-GenomeValidator:01	TARGET-15-SJMPAL043775.gv2.genome.fusions.somatic.small.summary.tsv	3			
TARGET-15-SJMPAL043775	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043775-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043775-09A-01D	DNA	EFO	SRS1761142	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043775-09A-01D A59143 library	PAIRED	GENOMIC	WGS	RANDOM	443	A59143	SRX2238850	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043775-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043775-09A-01D A59143 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59143_3_lanes_dupsFlagged_reheadered.bam	SRR4415906	@dbgap@:reads/SRP011999/SRS1761142/SRX2238850/SRR4415906/SRR4415906.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:02		TARGET-15-SJMPAL043775-09A-01D.indel.vcf	3						
TARGET-15-SJMPAL043775	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043775-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043775-09A-01D	DNA	EFO	SRS1761142	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043775-09A-01D A59143 library	PAIRED	GENOMIC	WGS	RANDOM	443	A59143	SRX2238850	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043775-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043775-09A-01D A59143 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59143_3_lanes_dupsFlagged_reheadered.bam	SRR4415906	@dbgap@:reads/SRP011999/SRS1761142/SRX2238850/SRR4415906/SRR4415906.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043775.quality_tagged.vcf	3						
TARGET-15-SJMPAL043775	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043775-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043775-09A-01D	DNA	EFO	SRS1761142	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043775-09A-01D A59143 library	PAIRED	GENOMIC	WGS	RANDOM	443	A59143	SRX2238850	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043775-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043775-09A-01D A59143 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59143_3_lanes_dupsFlagged_reheadered.bam	SRR4415906	@dbgap@:reads/SRP011999/SRS1761142/SRX2238850/SRR4415906/SRR4415906.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043775-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043775-09A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043775	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043775-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043775-09A-01D	DNA	EFO	SRS1761142	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043775-09A-01D A59143 library	PAIRED	GENOMIC	WGS	RANDOM	443	A59143	SRX2238850	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043775-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043775-09A-01D A59143 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59143_3_lanes_dupsFlagged_reheadered.bam	SRR4415906	@dbgap@:reads/SRP011999/SRS1761142/SRX2238850/SRR4415906/SRR4415906.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043775.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043775	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043775-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043775-09A-01D	DNA	EFO	SRS1761142	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043775-09A-01D A59143 library	PAIRED	GENOMIC	WGS	RANDOM	443	A59143	SRX2238850	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043775-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043775-09A-01D A59143 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59143_3_lanes_dupsFlagged_reheadered.bam	SRR4415906	@dbgap@:reads/SRP011999/SRS1761142/SRX2238850/SRR4415906/SRR4415906.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043775-09A-01D_TARGET-15-SJMPAL043775-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043775-09A-01D_TARGET-15-SJMPAL043775-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043775	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043775-09A	organism part	EFO	Bone Marrow	NCIt	"Primary Blood Derived Cancer - Bone Marrow"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043775-09A-01D	DNA	EFO	SRS1761142	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043775-09A-01D A59143 library	PAIRED	GENOMIC	WGS	RANDOM	443	A59143	SRX2238850	"WGS analysis of mixed phenotype acute leukemia sample TARGET-15-SJMPAL043775-09A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-06	TARGET-15-SJMPAL043775-09A-01D A59143 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59143_3_lanes_dupsFlagged_reheadered.bam	SRR4415906	@dbgap@:reads/SRP011999/SRS1761142/SRX2238850/SRR4415906/SRR4415906.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043775-09A-01D_TARGET-15-SJMPAL043775-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043775-09A-01D_TARGET-15-SJMPAL043775-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043775.combined_somatic_snvs.tab_delimited.txt	3
TARGET-15-SJMPAL043775	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043775-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043775-14A-01D	DNA	EFO	SRS1761199	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043775-14A-01D A59252 library	PAIRED	GENOMIC	WGS	RANDOM	422	A59252	SRX2238907	"WGS analysis of normal sample TARGET-15-SJMPAL043775-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043775-14A-01D A59252 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59252_2_lanes_dupsFlagged_reheadered.bam	SRR4415859	@dbgap@:reads/SRP011999/SRS1761199/SRX2238907/SRR4415859/SRR4415859.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01		TARGET-15-SJMPAL043775.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043775	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043775-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043775-14A-01D	DNA	EFO	SRS1761199	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043775-14A-01D A59252 library	PAIRED	GENOMIC	WGS	RANDOM	422	A59252	SRX2238907	"WGS analysis of normal sample TARGET-15-SJMPAL043775-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043775-14A-01D A59252 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59252_2_lanes_dupsFlagged_reheadered.bam	SRR4415859	@dbgap@:reads/SRP011999/SRS1761199/SRX2238907/SRR4415859/SRR4415859.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-StructVariant-DELLY:01		TARGET-15-SJMPAL043775.quality_tagged.vcf	3						
TARGET-15-SJMPAL043775	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043775-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043775-14A-01D	DNA	EFO	SRS1761199	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043775-14A-01D A59252 library	PAIRED	GENOMIC	WGS	RANDOM	422	A59252	SRX2238907	"WGS analysis of normal sample TARGET-15-SJMPAL043775-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043775-14A-01D A59252 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59252_2_lanes_dupsFlagged_reheadered.bam	SRR4415859	@dbgap@:reads/SRP011999/SRS1761199/SRX2238907/SRR4415859/SRR4415859.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01		TARGET-15-SJMPAL043775-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Tab:01	TARGET-15-SJMPAL043775-14A-01D.varFilter.eff.dbSNP_v137.COSMIC_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043775	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043775-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043775-14A-01D	DNA	EFO	SRS1761199	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043775-14A-01D A59252 library	PAIRED	GENOMIC	WGS	RANDOM	422	A59252	SRX2238907	"WGS analysis of normal sample TARGET-15-SJMPAL043775-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043775-14A-01D A59252 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59252_2_lanes_dupsFlagged_reheadered.bam	SRR4415859	@dbgap@:reads/SRP011999/SRS1761199/SRX2238907/SRR4415859/SRR4415859.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup-MutationSeq:01	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043775.combined_somatic_snvs.tab_delimited.txt	3						
TARGET-15-SJMPAL043775	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043775-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043775-14A-01D	DNA	EFO	SRS1761199	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043775-14A-01D A59252 library	PAIRED	GENOMIC	WGS	RANDOM	422	A59252	SRX2238907	"WGS analysis of normal sample TARGET-15-SJMPAL043775-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043775-14A-01D A59252 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59252_2_lanes_dupsFlagged_reheadered.bam	SRR4415859	@dbgap@:reads/SRP011999/SRS1761199/SRX2238907/SRR4415859/SRR4415859.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043775-09A-01D_TARGET-15-SJMPAL043775-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Indel:01	TARGET-15-SJMPAL043775-09A-01D_TARGET-15-SJMPAL043775-14A-01D.somatic.indel.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3			
TARGET-15-SJMPAL043775	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Childhood Mixed Phenotype Acute Leukemia	NCIt	Discovery	TARGET-15-SJMPAL043775-14A	organism part	EFO	Bone Marrow	NCIt	"Bone Marrow Normal"	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	St. Jude Children's Research Hospital	TARGET-15-SJMPAL043775-14A-01D	DNA	EFO	SRS1761199	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	TARGET-15-SJMPAL043775-14A-01D A59252 library	PAIRED	GENOMIC	WGS	RANDOM	422	A59252	SRX2238907	"WGS analysis of normal sample TARGET-15-SJMPAL043775-14A-01D using Illumina HiSeq 2500"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	BCCA	2016-05-11	TARGET-15-SJMPAL043775-14A-01D A59252 run	sequencing assay	EFO	250	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.18.66.3	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	A59252_2_lanes_dupsFlagged_reheadered.bam	SRR4415859	@dbgap@:reads/SRP011999/SRS1761199/SRX2238907/SRR4415859/SRR4415859.sra	2	GRCh37-lite	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01		TARGET-15-SJMPAL043775-09A-01D_TARGET-15-SJMPAL043775-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.vcf	3	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Tab-Snv:01	TARGET-15-SJMPAL043775-09A-01D_TARGET-15-SJMPAL043775-14A-01D.somatic.snv.dbSNP_v137.cosmic_v64.annotations.tab_delimited.txt	3	bcgsc.ca:Protocol:WGS-CombineSomaticSnvs:01	TARGET-15-SJMPAL043775.combined_somatic_snvs.tab_delimited.txt	3
