Adding af_gnomade flag to VEP annotation command

[evelyn-schmidt]

While @ksinghal28 was going through the process of documenting how the pipeline files were collected/created, we could not figure out how the gnomad_fixed_b38_exome.vcf.gz was created. The file is used in the VEP annotation step and seemed to be the V2 VCFs downloaded from the Gnomad Database but then some manual fixes were applied. These manual fixes and why they were needed are not clear.

A way to make up for some ambiguity of how we made this file is to just include a VEP flag that was added to a newer version -af_gnomade which adds the gnomad annotations in the way we were previously doing and also adding more possibility useful flags.

We would like user to be able to turn this option on/off in the yaml file.