The Variantstore is a Java/Groovy-based service application implemented using the Micronaut framework and enables storage and access to information on genomic variants and metadata from a connected database via a RESTful API.
- Import variants as Variant Call Format (VCF) files, annotated using SnpEff or VEP
- Import metadata in JSON together with variants (see Usage for details)
- Import gene information (Ensembl, GFF3 files)
- Support for MariaDB and PostgreSQL backend
- Query information on variants, genes, and cases via (secured) REST endpoints
- Ask Beacon endpoint if a specific variant exists in the store
- Export variants in Variant Call Format (VCF) and FHIR
See Documentation for the full detailed installation, run and configuration instructions.
Detailed documentation of the RESTful API is additionally available on SwaggerHub.
In the current version, the Variantstore service can be used with a MariaDB and PostgreSQL database. If you want to use a different DBMS, you have to provide an implementation for the VariantstoreStorage interface, make sure to use the same database model and set up the datasource accordingly in the application.yml.
If you would like to contribute to this pipeline or, please see the contributing guidelines.
For further information or help, don't hesitate to get in touch with us via mail or Twitter.
The Variantstore was created within the DIFUTURE (Data Integration for Future Medicine) Consortium.
This service was designed and implemented by Christopher Mohr. For a full list of authors, please refer to the file AUTHORS.