I have a rather large VCF file annotated using VEP, and I am trying to pick the most severe consequence of the variant for each variant in the file. Now I know that VEP automatically arranges the output to be listed as most-severe to least according to this (uswest.ensembl.org/info/genome/variation/prediction/predicted_data.html#consequences). However, my VCF doesn't have it in that format (no idea why, but I spot checked, and it doesn't) .
I cannot re-make the VCF using --severe because I didn't create it in the first place. My solution is to write a script to do this manually. But before I do that, I'd be interested if anyone out there has encountered a similar situation and have better suggestions for this.
Thanks for the help!