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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

  1. Fork it!
  2. Create your feature branch: git checkout -b my-new-feature
  3. Commit your changes: git commit -am 'Add some feature'
  4. Push to the branch: git push origin my-new-feature
  5. Submit a pull request :D

History

Project details


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