I see that GATK should not be used to call somatic variants from tumor/normal pairs:
Is this still true today? I ask because someone who is no longer in our group generated 'somatic calls' by
- calling SNPs on the normal
- calling SNPs on the matched tumor
- subtracting the normal SNPs from the tumor SNPs
I'm trying to determine how useful those calls are (probably not much).
This post from ~2 years ago also suggests that GATK should not be used for somatic calls: Difference Between Somatic And Germline Variant Calling?
Thanks everyone! Yes, I forgot to mention that I had already started running MuTect, which is also from Broad.
Try to refrain from posting thanks as an answer. An upvote or accepted answer will do just fine!