Feature request: Add VEP command

[naqvia]

Purpose/implementation Section

Briefly descibe the feature and provide meaningful references

Please add/document the appropriate VEP command to have the proper refseq column output.

What input data are required for this feature or analysis?

How do you plan to organise the feature or analysis - will it be a multi-function call or add to existing functions?

Who will complete the feature request (please add a GitHub handle here if relevant)?

[jharenza]

@rjcorb or @rebkau can you inform here please?

[jharenza]

or @jungkim2 do you have further details on this?

[jungkim2]

I used below for my annotation

vep --offline --cache --dir_cache $VEP_CACHEDIR --fasta $VEP_CACHEDIR/GRCh38.fa --use_given_ref --species homo_sapiens --assembly GRCh38 --fork 1 --xref_refseq --hgvs --hgvsg --canonical --symbol --distance 0 --exclude_predicted --flag_pick --lookup_ref --force --input_file testing_010423.vcf --output_file testing_010423_VEP.vcf --format vcf --vcf --no_stats --numbers

I believe the key here is we musth have --xref_refseq

[jharenza]

closed with #197