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Old 06-01-2012, 02:27 PM   #7
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Location: Burlington, VT

Join Date: Apr 2012
Posts: 8

Originally Posted by NGSNewbie1 View Post
Sorry for this newbie question but I haven't been able to get an answer after searching around. Is there a program that automagically produces the somatic mutations from inputted tumor and normal VCF files? I'm trying to avoid using a tool like SomaticSniper with BAM files because of size/computation etc. If I have the VCF files, is there an easy way to just select the differences?

Thank you in advance for any guidance!
While I'm uncertain that the results will really be what you're looking for, this can be done using GATK's SelectVariants with the --discordance flag (see for details).

Unfortunately, unless you already have GATK up and running, this is not a trivial task (as getting GATK functioning properly can be a bit tricky).

As mentioned by others though, tumor/normal paired variant calling generally seems to be carried out by a program specifically developed for that purpose (VarScan2, SMUG, and MuTect being the ones with which I am familiar).

Sorry there's not a better answer, but I hope this helps a bit.

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