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?