1678492347 / genomediver Goto Github PK

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