Seqcap ez exome v2

We counted the reads with each genotype at the 1000-genome SNP positions⁵⁵ in the normal and tumor exome sequencing data using alleleCounter (v.4.0.0). SNP positions overlapping the genomic ranges defined by {start-100} and end {end+100} target regions of the exome panel bed file (SeqCap EZ Exome v2, Roche Cat# 05860482001); SNP positions < 20X depth in the normal tissue were excluded.
From the read counts at those positions we derived the $BAF=\frac{\#ReadsB-allele}{\#ReadsA-allele+\#ReadsB-allele}$ and $LogR={log}_2\left(\frac{\#readsintumor}{averagedepthofcoverageintumor}\right)-{log}_2\left(\frac{\#readsinnormal}{averagedepthofcoverageinnormal}\right)$ as input to ASCAT. We ran ASCAT (v.2.5.2) on the BAF and LogR tracks⁵⁶ .We refitted the profiles by selecting the local optima (i.e. the minima in the total distance to integer DNA copy numbers) corresponding to the tumor ploidy that best matched the FACS-derived ploidy.

Capture was performed using SeqCap EZ Exome v2.0 (Roche Nimblegen) (n=86) and TruSeq Exome Enrichment Kit (Illumina) (n=3). Sequencing was performed using SOLiD™ 3.5 (n=8), SOLiD™ 4 (n=28), 5500xl SOLiD™ (n=12) (Life Technologies), GAIIX (n=2) and HiSeq (n=39) instruments (Illumina). Mapping to the human reference genome build hg19 was performed using BioScope v1.2 (SOLiD™ 3.5 data), BioScope v1.3 (SOLiD™ 4 data), LifeScope 2_5.1 (5500xl SOLiD™ data), bwa 0.6.2 (32 (link)) (GAIIX data), Novoalign (HiSeq data, n=40) and bwa 0.7.5a (HiSeq data, n=3). Local realignment was performed using the GATK 1.5-25 RealignerTargetCreator and IndelRealigner modules, duplicates were removed using Picard MarkDuplicates 1.29, and sorting and indexing were performed using SAMtools 0.1.8. Variant calling was conducted using the GATK 1.5-25 UnifiedGenotyper module. Variant calls were filtered to the capture target regions using BEDtools 2.16.2 (33 (link)) and bed files provided by the manufacturers. Further filtering was performed using FAVR (34 (link)). Annotation was performed using ANNOVAR (35 (link)).