https://github.com/molgenis/molgenis-app-genetics

Repository containing modules and features for interacting with, searching through, and visualising genetic data
https://github.com/molgenis/molgenis-app-genetics

genetics java javascript lifescience maven molgenis

Last synced: 2 days ago
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Repository containing modules and features for interacting with, searching through, and visualising genetic data

• Host: GitHub
• URL: https://github.com/molgenis/molgenis-app-genetics
• Owner: molgenis
• License: lgpl-3.0
• Created: 2017-04-20T10:25:27.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2022-12-06T23:36:18.000Z (almost 2 years ago)
• Last Synced: 2024-04-13T17:13:57.017Z (7 months ago)
• Topics: genetics, java, javascript, lifescience, maven, molgenis
• Language: Java
• Homepage:
• Size: 1.25 MB
• Stars: 1
• Watchers: 15
• Forks: 4
• Open Issues: 10
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# 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](https://github.com/molgenis/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