Varscan Somatic number and ProcessSomatic number difference

Question

[9521ljh]

Hi

i have normal-tumor.mpileup

i command on Linux:

java -jar Varscan.jar somatic Normal_tumor.remove0read.mpileup Somatic --mpileup 1 --output-vcf 1

output:

127,956 – Germline
8,593 – LOH
3,464 – Somatic
760 – Unknown

and i do ProcessSomatic which separate files based on somatic status and confidence:

java -jar Varscan.jar processSomatic Somatic.snp.vcf

java -jar VarScan.jar processSomatic Somatic.indel.vcf

output: 2572-Somatic / 377-Somatic

So i sum 2,572 + 377 = 2,909

Why number does not same? 2,909 != 3,464

Answer 1

[ATpoint]

Isolating Calls by Type and Confidence
The latest release of VarScan includes a new (undocumented) subcommand that will separate a somatic output file by somatic_status (Germline, Somatic, LOH). Somatic mutations will further be classified as high-confidence (.hc) or low-confidence (.lc). The command:

java -jar VarScan.jar processSomatic [output.snp]


The above command will produce 4 output files:

output.snp.Somatic.hc   (high-confidence Somatic mutations)
output.snp.Somatic.lc   (low-confidence Somatic mutations)
output.snp.Germline     (sites called Germline)
output.snp.LOH      (sites called loss-of-heterozygosity, or LOH)

Probably this shows the high-confidence somatics. Please read the documentation.