*** Contents ***

genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.1.somatic.maf - Reports all putative somatic variants detected across 248 UCEC tumor-normal pairs

*** Column Descriptions ***

[1-34] Standard MAF v2.3 columns as described at https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification
[35] transcript_name - The Genbank or Ensembl transcript ID onto which this variant was annotated
[36] strand - "+1" indicates forward strand, "-1" indicates reverse strand
[37] transcript_status - The reliability of this transcript (annotator uses this to select one among alternative isoforms)
[38] amino_acid_change - Change in the amino-acid at the locus, if any
[39] ucsc_cons - UCSC conservation score
[40] normal_depth - # of reads across this site in the normal sample
[41] normal_vaf - % of reads supporting the variant allele in the normal sample
[42] tumor_depth - # of reads across this site in the tumor sample
[43] tumor_vaf - % of reads supporting the variant allele in the tumor sample
[44] rna_depth - # of reads across this site in the tumor RNA-seq ('-' indicates RNA-seq unavailable)
[45] rna_vaf - % of reads supporting the variant allele in the tumor RNA-seq ('-' indicates insufficient data)
[46] polyphen - Polyphen's prediction of deleteriousness (using Ensembl VEP)
[47] sift - SIFT's prediction of deleteriousness (using Ensembl VEP)
[48] condel - Condel's consolidated prediction of deleteriousness (using Ensembl VEP)
[49] domain - Protein domain that the variant lies within (Protein DB names are prefixed)

*** Changelog ***

genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.1.5.0
> Added frameshift indels from ATR and RPL22 that were previously filtered out

genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.1.4.0
> Added a separate MAF for rare germline mutations across BRCA1, BRCA2, MLH1, MSH2, MSH4, MSH6, PMS1, PMS2, TP53, POLE
> The germline MAF was moved to protected storage: https://tcga-data-secure.nci.nih.gov/tcgafiles/tcgajamboree/awg_mafs/ucec/genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.1.4.0.tar.gz

genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.1.3.0
> Combined all somatic variants into a single MAF file
> Added RNA-seq VAFs and AA changes for each variant

genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.1.2.0
> Removed cases with evidence of low-level contamination
> Added more cases of endometrial serous histology

genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.1.1.0
> Combined somatic variants from 95 hypermutated and 144 not-so-hypermutated cases, into 1 MAF file
> Added a separate MAF for germline mutations across BRCA1, BRCA2, MLH1, MSH2, MSH6, PMS1, PMS2, TP53
> Germline MAF was later removed, and there's something called "mixed.somatic.maf" on the DCC - dunno what that is

genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.1.0.0
> First version with separate MAFs for 95 hypermutated cases, and 144 not-so-hypermutated cases
