Metadata-Version: 1.2
Name: genotype_variants
Version: 0.2.0
Summary: Project to genotype SNV, INDEL and SV.
Home-page: https://github.com/rhshah/genotype_variants
Author: Ronak Shah
Author-email: rons.shah@gmail.com
License: Apache Software License 2.0
Description: =================
        genotype_variants
        =================
        
        
        .. image:: https://img.shields.io/pypi/v/genotype_variants.svg
                :target: https://pypi.python.org/pypi/genotype_variants
        
        .. image:: https://img.shields.io/travis/rhshah/genotype_variants.svg
                :target: https://travis-ci.org/rhshah/genotype_variants
        
        .. image:: https://readthedocs.org/projects/genotype-variants/badge/?version=latest
                :target: https://genotype-variants.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        
        
        
        Project to genotype SNV, INDELS and SV.
        
        
        * Free software: Apache Software License 2.0
        * Documentation: https://genotype-variants.readthedocs.io.
        
        
        Features
        --------
        
        Currently this module only supports genotyping and merging small variants (SNV and INDELS).
        
        For this we have the following command line submodule called **small_variants**. 
        
        Which have the following sub-commands:
        
        * **generate**: To run GetBaseCountMultiSample on given BAM files
        * **merge**: To merge MAF format files w.r.t counts generated from the `generate` command.
        * **all**: This will run both of the sub-commands above `generate` and `merge` togather.
        * **multiple-patient**: This will run sub-commands `all` for multiple patients in the provided metadata file
        
        **Please read the USAGE** (https://genotype-variants.readthedocs.io/en/latest/usage.html) **section of the documentation for more information**
        
        To Do
        -----
        
        * Tagging genotyped files for thresholds
        * Genotyping normal buffy coats
        * Genotype structural variants calls
        
        
        Credits
        -------
        
        This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
        
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
        
        
        =======
        History
        =======
        
        0.1.0 (2020-01-30)
        ------------------
        
        * First release on PyPI.
        
Keywords: genotype_variants
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.5
