I have a variant set annotated by GATK's Funcotator... creates an extra field in the VCF called "Funcotator" with several annotations separated by pipe characters. I want to get some statistics on % intronic vs exonic and missense/nonsense mutations. Is the easiest way to do this using grep? Or does GATK's SelectVariants work?
There are a few ways you can do this. I'd recommend grabbing a script that I wrote to turn Functoator VCF annotations into CSVs.
I did this so that I could more easily debug things when I was writing it.
The script is here: createFuncotationCsvFromFuncotatorVcf.sh