How to extract only TUMOR variants from vcf file?

Question

[Fill]

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

Answer 1

[igor]

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]

[Fill]

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

[Nikleotide]

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