Find GeL Tier 3 variants with Green PanelApp genes
Project description
jellypy-tierup
tierup
is a jellypy module for reanalysing Tier 3 variants from GeL 100KG cases.
Documentation
https://acgs.gitbook.io/bioinformatics/jellypy-docs
Installation
pip install ./tierup
Usage
tierup -i 12354-1 -c tierup_config.ini
The tierup_config.ini
file format:
[pyCIPAPI]
pyCIPAPI_USERNAME = me
pyCIPAPI_PASSWORD = pass
[tierup]
tierup_STDOUT = TRUE
tierup_IRJOUT = /home/Documents/interpretation_requests
Note: In the usage example above, access to the NHS N3 network is required for TierUp to download interpretation request data. Pass pre-existing data in GEL v6 json format as follows:
tierup --json 12354-1.json --config tierup_config.ini
Contributing
- Fork it!
- Create your feature branch: git checkout -b my-new-feature
- Commit your changes: git commit -am 'Add some feature'
- Push to the branch: git push origin my-new-feature
- Submit a pull request :D
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