MuTect -> vcf pipeline?option?

[dkrtndhkd]

Hi, is there anyone who know the option of MuTect which gives a VCF formed result to users?

I know that we can modify the result of MuTect by switching and copying certain column,

but the extra column of VCF form also tells us lots of valuable information.

[dakl]

Hey all,

I have the same issue. MuTect works great, but I need the output in VCF format for snpEff downstream. Writing my own parser seems... well not. so. fun.

Does anyone have a good solution for this?

BR
Daniel

[sleight82]

MuTect can output vcf natively; just supply the "--vcf" parameter with an output file.