Repeat Expansion Specification Files

The repeat-specification (also called variant catalog) JSON file defines the repeat regions for ExpansionHunter to analyze. Default repeat-specification for some pathogenic repeats are in the /opt/edico/repeat-specs/_directory (based on the reference genome used with DRAGEN).

You can create specification files for new repeat regions by using one of the provided specification files as a template. See the ExpansionHunter documentation for details on the format.

`--repeat-genotype-specs` is required for ExpansionHunter. If the option is not provided, DRAGEN will attempt to auto-detect the applicable catalog file from /opt/edico/repeat-specs/ based on the reference provided.