How to extract only TUMOR variants from vcf file?
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5.4 years ago
Fill ▴ 70

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 • 2.4k views
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5.4 years ago
igor 13k

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]

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

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

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