This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to extract only TUMOR variants from vcf file?

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

vcf vcftools
• 3,449 views • link
written by Fill Fill

1 answer

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]

• 0 views • link
written by igor igor

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

• 0 views • link
written by Fill Fill

Log in to answer this question.

More posts like this