Pathogenic Variant Filtering

This module filters variants for pathogenicity based on a set of criteria.

Installation

Installation through Oakvar

From Oakvar store:

ov module install just_pathogenic

From a direct link on GitHub:

ov module install just_pathogenic --url https://github.com/dna-seq/just_pathogenic/tree/main

Debugging notes

If you want to debug the module, then use the conda/micromamba environment where oakvar is installed (for example quick-dna).

micromamba activate quick-dna

Then you can run the module with:

ov run -p just_pathogenic