Question: How to extract only TUMOR variants from vcf file?
gravatar for Fill
2.2 years 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 • 1.3k views
ADD COMMENTlink modified 2.1 years ago • written 2.2 years ago by Fill70
gravatar for igor
2.2 years ago by
United States
igor8.3k 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 2.2 years ago by igor8.3k

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

ADD REPLYlink written 2.2 years ago by Fill70

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

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Nikleotide100
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