How to best predict effect for each variant and count specific effect found in each individual using variant effect predictor?

Question

[optimistsso4co3]

I have multiple .vcf files for individuals (also have merged.vcf with all indivs.). I would like to predict each variants effect and then count variants with, e.g. IMPACT=HIGH.

Is there an automated tool to do such workflow for any kind of variable i wan't to compare between individuals?

[Emily]

This isn't something the VEP can do, but if you get your VEP output in VCF you could try VCFTools.