The GA4GH Variation Representation Specification provides a comprehensive framework for the computational representation of biological sequence variation. VR-Spec is the result of a collaboration among contributors representing national information resource providers, major international public initiatives, and diagnostic testing laboratories.
NOTE: vr-spec is under very active development. The priorities and roadmap are available at the VR 2019 Project.
- 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 VR model is the product of the GA4GH Variation Representation group.
SEE ALSO: See vr-python for an implementation and Jupyter notebooks.
The schema is available in the schema/ directory, in both yaml and
json versions. It conforms to json schema draft-07. For a list of
libraries that support json schema, see JSON
Schema>Implementations.
VR uses yaml as the source document for json schema
To convert vr.yaml to vr.json:
make vr.json
You'll probably have to pip install pyyaml first.
To watch for changes and update automatically:
make -C schema watch &
The VR specification documentation is written in reStructuredText and
located in docs/source/. Commits to this repo are built
automatically at vr-spec.readthedocs.io__.
To build documentation locally, type:
make -C docs 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.)