I'm working on a DNAseq germline workflow to make calls for other researchers to use. I note that GATK's Best Practices uses Funcotator to annotate their germline calls, one of my colleagues has used VEP for this purpose, and I know we've also used SnpEff in the past, but it's been a while. Googling has failed me for recent comparisons: are there big differences in results between using one or the other? Any compelling reasons to pick? Should I run multiple ones?
I've set up Funcotator and it's working, and I have a VEP cache set up for other workflows, but I recall it being super finicky to setup.