seqr is a software package for working with next generation sequencing data, specifically in the context of studying rare genetic diseases.

This package contains the analysis code that powers the seqr website, but we welcome anyone wishing to set up their own private instance of seqr.

Please Note: This package is in active development, and the API is extremely unstable. We suggest you contact us if you want to build on this repo.

• seqr local install: deploy/mac_osx/README.md
• phenotips integration instructions: PHENOTIPS_INTEGRATION.md enable PhenoTips to be used to enter HPO-based phenotypes from within seqr.

Current big-picture refactoring plans include:

• refactor meta-data schema to better support multiple samples per individual (eg. for individuals that have both WGS and whole exome variant calls).
• refactor the UI to use React.js
• move from mongodb to a different backend that's better-optimized for our requirements (currently investigating open-source Apache tools like Solr, as well as managed cloud databases)