VEP cache

Genome reference files can consume large amounts of storage. Many users of SOPRANO may have existing VEP caches with genome references therein, that could be used directly by SOPRANO.

To this end, users can link their existing reference files to the SOPRANO Ensembl downloads folder ensembl_downloads/.

Users should run:

soprano-link-vep [-h] [--cache SRC_CACHE]

-h | --help

Get help output

-c | --cache

Provide the path to the ensembl vep cache. (default: /home/USER/.vep)

The cache argument is useful if you have cached VEP data into a non-standard location.