https://github.com/ga4gh/vrs

Extensible specification for representing and uniquely identifying biological sequence variation
https://github.com/ga4gh/vrs

bioinformatics genomics variation

Last synced: 4 months ago
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Extensible specification for representing and uniquely identifying biological sequence variation

• Host: GitHub
• URL: https://github.com/ga4gh/vrs
• Owner: ga4gh
• License: apache-2.0
• Created: 2016-08-31T05:09:01.000Z (almost 10 years ago)
• Default Branch: v2
• Last Pushed: 2025-12-20T21:02:29.000Z (6 months ago)
• Last Synced: 2025-12-22T14:24:04.880Z (6 months ago)
• Topics: bioinformatics, genomics, variation
• Language: Jupyter Notebook
• Homepage: https://vrs.ga4gh.org
• Size: 8.91 MB
• Stars: 94
• Watchers: 24
• Forks: 38
• Open Issues: 34
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Codeowners: .github/CODEOWNERS

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README

          
# Variation Representation Specification (VRS)

[![DOI](https://zenodo.org/badge/67005248.svg)](https://zenodo.org/badge/latestdoi/67005248)

[![Read the Docs](https://img.shields.io/readthedocs/vr-spec/1.1)](https://vrs.ga4gh.org/)

[![tests](https://github.com/ga4gh/vrs/actions/workflows/tests.yml/badge.svg)](https://github.com/ga4gh/vrs/actions/workflows/tests.yml)

The [GA4GH](https://www.ga4gh.org/) [Variation Representation Specification](https://vrs.ga4gh.org/)

provides a comprehensive framework for the computational representation of biological sequence

variation. VRS is the result of a collaboration among [contributors](CONTRIBUTORS.md) representing

national information resource providers, major international public initiatives, and diagnostic

testing laboratories.

VRS is licensed under the [Apache License 2.0](LICENSE).

> **NOTE:** VRS is under active development.

> See the [VRS Project Roadmap](https://github.com/orgs/ga4gh/projects/12).

## 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](./validation/) to ensure consistency of implementations.

The VRS model is the product of the [GA4GH Variation Representation group](https://www.ga4gh.org/product/variation-representation/).

> **SEE ALSO**: See [VRS-Python](https://github.com/ga4gh/vrs-python) for a Python

> implementation and Jupyter notebooks.

## Using the schema

The schema is available in the [schema/](./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](https://json-schema.org/tools).

## Installing for development

Fork the repo at .

    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](./schema/vrs/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](docs/source/). Commits to this repo are built automatically at .

To build documentation locally, you must install [entr](https://eradman.com/entrproject/):

    brew install entr

Then from the root directory:

    cd docs

    make clean watch &

Then, open [docs/build/html/index.html](./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/](./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/](./validation/)) provide language-neutral tests for those implementing

tools with VRS.

To run the smoke tests:

    make test