Varscan Somatic number and ProcessSomatic number difference
1
0
Entering edit mode
3.5 years ago
9521ljh ▴ 50

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

SNP sequencing alignment genome • 1.7k views
ADD COMMENT
0
Entering edit mode
3.5 years ago
ATpoint 65k
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.

ADD COMMENT

Login before adding your answer.

Traffic: 1343 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6