VarScan output different when choosing VCF and variant missing?
0
0
Entering edit mode
9.0 years ago
Pascal ▴ 250

Hi,

I am using VarScan version 2.3.7 for variant calling in my tumour samples. Depending if I choose VCF as output I seem to get different results. Here is an example on a specific position where I am expecting to find one somatic mutation, but get none in both cases:

java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup -l region.bed -q 1 -B -f GRCh37-lite.fa normal.bam  tumour.bam) output.txt --mpileup 1

Result is:

681 positions in mpileup file
366 had sufficient coverage for comparison
365 were called Reference
0 were mixed SNP-indel calls and filtered
1 were removed by the strand filter #Note this line
0 were called Germline
0 were called LOH
0 were called Somatic
0 were called Unknown
0 were called Variant

Same for VCF output:

java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup -l region.bed -q 1 -B -f GRCh37-lite.fa normal.bam  tumour.bam) output.txt --mpileup 1 --output-vcf

Result is:

681 positions in mpileup file
366 had sufficient coverage for comparison
365 were called Reference
0 were mixed SNP-indel calls and filtered
0 were removed by the strand filter
0 were called Germline
0 were called LOH
1 were called Somatic #Note this line
0 were called Unknown
0 were called Variant

However, the result files are empty in both cases (apart from the header).

Help is highly appreciated.

Pascal

VarScan VCF Exome-Seq Variant-Calling • 4.7k views
ADD COMMENT
0
Entering edit mode

Just tried version 2.3.1. With both options 1 somatic mutation is reported and both output files contain this mutation.

ADD REPLY
0
Entering edit mode

Did you manage find the reason for this behaviour? Would be interested to how that might happen.

ADD REPLY
0
Entering edit mode

No, I wasn't able to track down what happens there.

ADD REPLY

Login before adding your answer.

Traffic: 1030 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