View Single Post
Old 06-12-2012, 10:10 AM   #8
shyam_la
Member
 
Location: California

Join Date: Mar 2012
Posts: 97
Default

Quote:
Originally Posted by SkinFlayer View Post
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 http://www.broadinstitute.org/gsa/ga...tVariants.html 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.

Jason
Hi,

Do you know how to annotate the output from MuTect? I have 3800 mutation calls and I am stuck..
shyam_la is offline   Reply With Quote