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CharGer: clinical Characterization of Germline variants.

ABSTRACT: SUMMARY: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. AVAILABILITY AND IMPLEMENTATION:Source code is freely available at https://github.com/ding-lab/CharGer and is distributed under the GNU GPL-v3.0 license. Software is also distributed through the Python Package Index (PyPI) repository. CharGer is implemented in Python 2.7 and is supported on Unix-based operating systems. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

SUBMITTER: Scott AD

PROVIDER: S-EPMC6394391 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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CharGer: clinical Characterization of Germline variants.

Scott Adam D AD Huang Kuan-Lin KL Weerasinghe Amila A Mashl R Jay RJ Gao Qingsong Q Martins Rodrigues Fernanda F Wyczalkowski Matthew A MA Ding Li L

Bioinformatics (Oxford, England) 20190301 5

<h4>Summary</h4>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 cla ...[more]

PMID: 30102335

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