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: