VEP annotation for joint VCFs?

General
1

Hello,

I was able to extract allele counts and VEP annotations from the exome VCF tables, and I wanted to do the same for the the joint VCF tables, but I realized the VEP annotation is not included?

What is the recommended way to obtain the VEP annotation for the variants in the joint VCF files? Should I use the exome/genome files, or some other set of files?

Thanks!

2

Yes, we recommend extracting the VEP annotations from the exome and genome files. Another resource that might be useful is the Browser variants Hail Table.