Annotation database#

The oligogenic pipelines rely on an annotation database for quick retrieval of the variant, gene and gene pair input features for VarCoPP.

We currently offer limited access to such a database for use in this package. If you wish to get access, please email us so that we can provide you with credentials.

Pass credentials to oligopipe#

As command-line arguments:

Annotation database credentials:
  -host DB_HOST, --db-host DB_HOST
                        Hostname of annotation database server.
  -u DB_USER, --db-user DB_USER
                        User for annotation database.
  -pw DB_PASSWORD, --db-password DB_PASSWORD
                        Password for annotation database.
  -p DB_PORT, --db-port DB_PORT
                        Port for annotation database.

In the config YAML:

annotation_database:
  host:
  user:
  password:
  port: