Gene panels

NOTE

This documentation is a work in progress and is incomplete.

Please contact developers for more details.

Everything in ELLA revolves around gene panels, and they're an essential part of the configuration. Note that a gene panel doesn't have to be a targeted panel in the traditional sense, but can include all genes in the exome if desired.

A gene panel includes, among other things, the following:

• A list of transcripts, with associated gene name/id and transcript + exon coordinates
• A list of phenotypes, with associated inheritance pattern

To add a new gene panel, run the following command:

ella-cli deposit genepanel --folder <path to gene panel directory>

Note that <PanelName>_<version>.transcripts.csv and <PanelName>_<version>.phenotypes.csv files are required.

See src/vardb/testdata/clinicalGenePanels/ for example gene panels and naming conventions.