These files represent the latest LOHcate analysis results for TARGET-AML, run on Jan 29, 2014.  The provided include: 
(1) VAF_2D.zip zipped two-dimensional variant-allele-fraction (VAF) plots, in which the VAF from sites in the matched normal is plotted against the 
VAF values from sites in the tumor, enabling direct, comparative visualization of copy number events;
(2) VAF_Genomewide.zip zipped genome-wide VAF plots per sample, in which genomic coordinate is plotted on the x-axis, while the VAF value for that site 
is plotted on the y-coordinate; the color of the point indicates the called copy number event...the event classifications include:

      Event classifications:
      a)      LOH - if their VAF values deviate significantly from the expected value of 0.5, and the total copy number < 1.8
      b)      GainSomatic (somatic gain) - if their VAF values deviate significantly from the expected value of 0.5, and the total copy number >= 2.2
      c)      cnLOH (copy neutral LOH) - if their VAF values deviate significantly from the expected value of 0.5, and 1.8 <= total copy number < 2.2
      d)      HetSomatic (somatic mutations) – if normal VAF < 0.1 and tumor VAF > 0.1
 
Also provided are two tables in tab-delimited format:
(3) gene_enrichment.target_aml.txt – This file indicates events by patient per gene.  For example, column  I (LOH_recurrence) indicates the number of patients 
who exhibit LOH in at least one site within the indicated gene (given by row).  Likewise for columns H, J, and K.  Column F (LOH_or_cnLOH_refLost) indicates 
the number of patients who exhibit LOH (or cnLOH) in at least one site (such that the reference allele is lost, and the variant allele remaining is not a common 
variant) within the indicated gene.  Column F should not exceed Columns I+J.  Column G (in the format of “chromosome_position1:count,chromosome_position2:count,…”) 
indicates the sites involved in Column F.  Note that G may exceed F, as multiple sites per patient may be involved.
(4) eventsByPatientPerGene.target_aml.txt – This file provides a complete set of tuples:  (gene, event, patient), which comprises the counts in gene_enrichment.target


These calls were made by LOHcate, which can be referenced by:
 
Dewal, N et al. LOHcate: Robust detection and analysis of aneupoidy in whole exome sequence data from cancer genomes.  In preparation
