Refactor vep process to support different commands and versions - HIGH PRIORITY (CLIN-3407)

[LysianeBouchard]

Description of feature

We should limit hard-coded command line options to the minimum.

If possible, we would like the implementation to work with other VEP versions (>= v103). This means that if we switch the Docker container to one matching an older VEP version, it should still function correctly. If this requires too much effort, it can be addressed in a dedicated issue.

See https://ferlab-crsj.atlassian.net/browse/CLIN-3407