[Breaking Change] VEP configuration format has changed


#1

The VEP configuration format has changed to be more flexible. The new format is documented with the vep command.

On Google Cloud Platform, cloudtools --vep option currently installed VEP v85 database files for reference GRCh37. The corresponding configuration file is gs://hail-common/vep/vep/vep85-gcloud.json and vep should be invoked as

vep_result = hl.vep(mt, 'gs://hail-common/vep/vep/vep85-gcloud.json')

The init script also copies the configuration file locally to the master node file:///vep/vep85-gcloud.json, so that can also be used as the configuration path. The init script will continue to copy the old properties file to /vep/vep.properties to continue support versions of Hail before this change.