Hello. I'm using varscan2 for germline calling.I have questions about using varscan options.
my data is tumor-normal paired HCC WXS DNA bams.
First, I made mpileup file by using samtools.
samtools mpileup [normal bam] [tumor bam] -B -q 1 > [normal-tumor.mpileup]
Second, I'll run varscan.
java -jar VarScan.jar somatic [normal-tumor.mpileup] [output] --mpileup 1 OPTIONS
varscan2 output have germline calling/somatic calling/ LOH. so I will use germline calling only.
In nature article (Integrated analysis of germline and somatic variants in ovarian cancer, Krishna L. Kanchi et al. 2013 ), they used following varscan options for germline calling of tumor-normal paired samples.
"Germline SNPs and indels were identified in paired BAMs using VarScan2 with the following parameters: min-coverage=30, min-var-freq=0.08, normal-purity=1, P-value=0.10, somatic-P-value=0.001 and validation=1. Additional germline SNPs were identified using Samtools (version 0.1.7a (revision number 599) and additional germline indels were identified using GATK (version 1.0 (revision 5336)."
Varscan2 manual's default P-value is 0.99, but in article they use 0.10.
which options are important and which value is good when I use germline calling with varscan2 somatic?