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Published 20 hours ago • verified publisher icon nf-core

vcf to maf conversion

Open kunstner opened this issue 1 year ago • 2 comments

Description of feature

Hi,

I was wondering whether it is possible to integrate vcf2maf as well into sarek to directly convert annotated vcf files to maf.

https://github.com/mskcc/vcf2maf

Best, Axel

kunstner avatar Oct 11 '22 06:10 kunstner

Yes we have talked about it quite a bit. However, before we do that we need to find a solution for snpeff annotated files and the merged ones. vcf2maf only works for VEP.

FriederikeHanssen avatar Oct 11 '22 07:10 FriederikeHanssen

Many thanks for the quick reply. Right, the conversion is VEP only. I've forgotten that issue.

kunstner avatar Oct 11 '22 09:10 kunstner