Hi there, 

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 (http://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! 
Hi shwethacm,

I'm afraid that I'm not able to help with any particular suggestions or custom scripts that will help to filter or rearrange your VCF output. However, I wanted to correct a small error in your assumption- the VEP does not necessarily arrange the output from most to least severe for each variant.

Some considerations for your filtering and reordering:

 - You may be able to run your VCF through the VEP again using the different --pick options:
http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#filt
 - You may be able to use the filter_vep script to filter your results:
http://www.ensembl.org/info/docs/tools/vep/script/vep_filter.html

Best wishes

Ben
Ensembl Helpdesk