genomenexus/gn-vep repository overview

Genome Nexus VEP is a rest wrapper around Ensembl's Variant Effect Predictor (VEP) CLI tool.

⁠As of Genome Nexus VEP Version 3.0.0:

There is a new required environment variable: MODE that may be set to either cache or database. You must provide the same environment variables as specified in the 2.0.0 section.

⁠Cache Mode

You must pass a FASTA_FILENAME environment variable specifying the name of the FASTA file downloaded from Ensembl. You must also mount the VEP cache file to the cache-data directory of the docker image.

⁠Database Mode

Besides specifying the MODE as database nothing has changed.

⁠As of Genome Nexus VEP Version 2.0.0:

The naming convention for tags will adhere to the following schema: {VEP_VERSION}-{GENOME_NEXUS_VEP_VERSION}. Additionally, some tags may be marked as extended indicating that these versions also support PolyPhen predictions, SIFT predictions, and AlphaMissense pathogenicity scores. If you do not require this data, it is recommended to the base version of these images.

⁠Running the Image

The application will run on container port 8080, so be sure to expose this port to allow connections from any external applications.

In order to run Genome Nexus VEP, you must connect to the homo_sapiens_core database provided by Ensembl. For more information on setting up this database, please refer to the Genome Nexus VEP GitHub Repository⁠

Additionally, you must provide the following environment variables to indicate the database connection settings VEP should use:

• MYSQL_USER
• MYSQL_PASSWORD
• MYSQL_HOST
• MYSQL_PORT