MuTect -> vcf pipeline?option?

dkrtndhkd

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Join Date: Jan 2012

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#1

MuTect -> vcf pipeline?option?

08-03-2012, 08:56 AM

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.
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dakl

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#2

10-12-2012, 05:28 AM

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
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sleight82

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#3

05-22-2013, 07:41 AM

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