This repository contains the backend and frontend code for Genome Diver, a tool for variant prioritization using HPO phenotypes and genotypes.
Server requires installation Postgres 11+, Nextflow, and Java 8
- Postgres is required to store user info, patient data, analysis runs and a searchable copy of the HPO ontology.
- Nextflow is required to run the analysis on the submitted variant and phenotype information.
- Analysis pipelines require an installation of Exomiser, Picard, VCFAnno, and Clinvar
- GenomeDiver filters are located in a separate project.
- Server application started by sbt via sbt run or sbt reStart
- Server configuration is largely specified by resources/application.conf
- Database scripts are located in the database directory which facilitates the loading of HPO ontology and annotations.
- Example Nextflow configurations are included in the nextflow/ directory
- Default Exomiser configuations as well as adjustable parameters for filters are located in nextflow/templates directory
- Migrate away from custom filters and use Exomiser 12
- For phenotype recommendation LIRICAL should be used