Question: VarScan output different when choosing VCF and variant missing?
0
gravatar for Pascal
4.7 years ago by
Pascal250
European Union
Pascal250 wrote:

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
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
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

 

 

ADD COMMENTlink written 4.7 years ago by Pascal250

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

ADD REPLYlink written 4.7 years ago by Pascal250

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

ADD REPLYlink written 4.4 years ago by sginzel0

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

ADD REPLYlink written 4.4 years ago by Pascal250
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