Categorical Variation Representation Specification (Cat-VRS)

The GA4GH Categorical Variation Representation Specification provides a A terminology and data model for describing categorical variation concepts, built on top of the GA4GH Variation Representation Specification (VRS). Cat-VRS is the result of a collaboration among contributors representing national information resource providers, major international public initiatives, and bioinformatics laboratories.

Cat-VRS is licensed under the Apache License 2.0.

Test Set

Categorical variant classes intended to be covered by this specification can be appended to this CatVar test set document to direct future specification development efforts.

Using the schema

The schema is available in the schema/ directory, in both yaml and json versions. It conforms to JSON Schema Draft 2020-12. For a list of libraries that support JSON schema, see JSONSchema>Tools.

Installing for development

Fork the repo at https://github.com/ga4gh/cat-vrs.

git clone --recurse-submodules git@github.com:YOUR_GITHUB_ID/cat-vrs.git
cd cat-vrs
make devready
source venv/3.12/bin/activate

If you already cloned the repo, but forgot to include --recurse-submodules you can run:

git submodule update --init --recursive

Contributing to the schema

Cat-VRS uses cat-vrs-source.yaml as the source document for JSON Schema.

To create the corresponding def and json files after making changes to the source document, from the root directory:

cd schema
make all

Contributing to the docs

The Cat-VRS specification documentation is written in reStructuredText and located in docs/source. Commits to this repo are built automatically at https://vrsatile.readthedocs.io/en/latest/catvars/index.html#.

To build documentation locally, you must install entr:

brew install entr

Then from the root directory:

cd docs
make clean watch &

Then, open docs/build/html/index.html. The above make command should build docs when source changes. (Some types of changes require recleaning and building.)