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All Projects → ding-lab → Charger

ding-lab / Charger

Licence: gpl-3.0
Characterization of Germline variants

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python
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CharGer

⚠️ NOTICE: To use the most recent stable CharGer (version v0.5.4; Python 2.7 only), please refer to the installation instructions and source code at commit 7d7d291 or tag v0.5.4. Python 3 compatible CharGer is still under development.

CharGer (Characterization of Germline variants) is a software tool for interpreting and predicting clinical pathogenicity of germline variants. CharGer gathers evidence from databases and annotations, provided by local tools and files or via ReST APIs, and classifies variants according to ACMG guidelines for assessing variant pathogenicity. User-designed pathogenicity criteria can be incorporated into CharGer’s flexible framework, thereby allowing users to create a customized classification protocol.

If you use CharGer, please cite our publication so we can continue to support CharGer development:

Scott, A.D., Huang, K.-L., Weerasinghe, A., Mashl, R.J., Gao, Q., Martins Rodrigues, F., Wyczalkowski, M.A., and Ding, L. (2018). CharGer: clinical Characterization of Germline variants. Bioinformatics 35, 865–867. DOI: https://doi.org/10.1093/bioinformatics/bty649

Installation

⚠️ Version 0.6.0+ is still UNDER DEVELOPMENT and INCOMPLETE.

CharGer requires Python 3.6+. Use pip to install CharGer:

pip install charger

Alternatively, use conda with bioconda channels configured:

conda install charger

Usage

charger -h

Visit CharGer's documentations for its detailed usage.

License

CharGer is made by Ding Lab under GNU GPL v3.0 only license.

Note that the project description data, including the texts, logos, images, and/or trademarks, for each open source project belongs to its rightful owner. If you wish to add or remove any projects, please contact us at [email protected].