Parsing through VCF annotated by Funcotator

Question

[abbysue]

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?

Answer 1

[jonnsmith]

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

That should work for you (though it may not work correctly if the VCF header is very large). If you have more troubles you can post over on the GATK forums or open a question ticket on GitHub.