Question: How to extract only TUMOR variants from vcf file?
gravatar for Fill
20 months ago by
Fill70 wrote:

Hi everyone

I have a vcf file with normal+tumor variants after varscan. I need only tumor variants, so I tryed to do

vcftools --vcf ... --out ... -c TUMOR

but it doesn't work.

I really appreciate any help

Thanks in advance

vcftools vcf • 1.1k views
ADD COMMENTlink modified 20 months ago • written 20 months ago by Fill70
gravatar for igor
20 months ago by
United States
igor7.4k wrote:

There are instructions given in the VarScan documentation for extracting somatic mutations:

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]

ADD COMMENTlink written 20 months ago by igor7.4k

Thank you for respond, but the question is how to correct already exsiting vcf file with tumor and normal samples.

ADD REPLYlink written 20 months ago by Fill70

I think this thread has the answer to your questiom. Extract subset of samples from multigenome vcf file

ADD REPLYlink modified 20 months ago • written 20 months ago by Nikleotide70
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