molgenis / molgenis-app-genetics

Repository containing modules and features for interacting with, searching through, and visualising genetic data

molgenis-genetics

This repository contains modules designed for viewing, filtering, annotating, visualising, and querying genetic data.

Code is built using v4.0.0 of the MOLGENIS platform

Deploying GeneNetwork application

After deploying the molgenis-genetics WAR to a server, follow these steps to get the GeneNetwork application running

1. Import HPO ontology
2. Configure a MatrixMetadata entity with the following files
   • matrix file: GeneNetwork.txt Giant matrix containing GeneNetwork scores for HPO - Ensembl Gene combinations
   • rowMappingFile: mart_export.txt Translation file between HGNC Gene symbols and Ensembl Gene identifiers
3. Import a VCF via the GAVIN annotation plugin
4. View results

In the gene-network/patients/[id] screen, you can search for HPO phenotypes. Depending on GeneNetwork scores for each variant, the table is sorted

Configuring GAVIN annotation for VCF files

If you enable the 'diagnostics' plugin in the menu, it will allow you to annotate your VCF files with GAVIN. You will need the following resources to do this:

1. SnpEff.jar
2. CADD.tsv.gz
3. exac.vcf.gz
4. GAVIN_calibrations_r0.3.xlsx