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Variation Representation Specification (VRS)

DOI Read the Docs tests

The GA4GH Variation Representation Specification provides a comprehensive framework for the computational representation of biological sequence variation. VRS is the result of a collaboration among contributors representing national information resource providers, major international public initiatives, and diagnostic testing laboratories.

VRS is licensed under the Apache License 2.0.

NOTE: VRS is under active development. See the VRS Project Roadmap.

Specific goals

  • Develop common language- and protocol-neutral information models and nomenclature for biological sequence variation.
  • From the information models, develop data schemas. The current schema is defined in JSON Schema, but other formats are expected.
  • Provide algorithmic guidance and conventions to minimize representational ambiguity.
  • Define a globally unique computed identifier for covered data classes.
  • Develop validation tests to ensure consistency of implementations.

The VRS model is the product of the GA4GH Variation Representation group.

SEE ALSO: See VRS-Python for a Python implementation and Jupyter notebooks.

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/vrs.

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

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

git submodule update --init --recursive

Contributing to the schema

VRS uses 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

Note: We have a custom pre-commit hook to run these commands after you stage a source document

Contributing to the docs

The VRS specification documentation is written in reStructuredText and located in docs/source. Commits to this repo are built automatically at https://vrs.ga4gh.org.

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.)

Testing

The VRS repo contains two kinds of tests. Basic smoke tests in tests/ ensure that the schema is parsable and works with certain tools. These tests provide a basic sanity check during development.

Validation tests (in validation/) provide language-neutral tests for those implementing tools with VRS.

To run the smoke tests:

make test