variantgrid

What it does

VariantGrid is a database and web application for storing, analysing and classifying genetic variants. Users upload VCF files and the system automatically annotates them with Ensembl VEP, shows every sample from all uploaded VCFs that share a given variant, and supports real time drag and drop interactive analyses of samples, trios or cohorts. Variants can be classified with a customizable ACMG form, and the application manages curation data including patient phenotypes. A screenshot in the README shows the analysis interface, giving a sense of the web based workflow.

Reference builds and instances

The database holds GRCh37, GRCh38, Ensembl and RefSeq references together, with some automatic conversion between them. Beyond a private install, the project points to several shared servers: a research focused public instance at variantgrid.com with free user access, the Shariant Australia variant interpretation sharing server, and RUNX1Db for rare blood disease data sharing. These demonstrate both research and clinical collaboration use. SA Pathology uses it for clinical or diagnostic work, and labs at the Centre for Cancer Biology use it for research exomes, according to the README.

Licensing and stack

VariantGrid code is free to use for research and evaluation, while production commercial use requires a licence that the README says will make the code fully free and open source after four years. The project invites contact to discuss support or collaboration and offers managed cloud instances as well as source or VM based installation. Technically it is written in Python 3 using Django and PostgreSQL, and the README links a read the docs user guide and a wiki covering installation and maintenance. The open issues count in the README sits high, reflecting an actively used but not fully closed out issue tracker.

Editorial conclusion

The application is built on Python 3 with Django and PostgreSQL and is used by SA Pathology for diagnostic work and by Centre for Cancer Biology labs for research exomes.