Metadata-Version: 2.4
Name: genotype-variants
Version: 0.3.10
Summary: A tool for genotyping SNV, INDEL, and SV variants in genomic data.
Author-email: Ronak Shah <rons.shah@gmail.com>
License: Apache-2.0
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Healthcare Industry
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Requires-Python: >=3.9
Description-Content-Type: text/x-rst
License-File: LICENSE
License-File: AUTHORS.rst
Requires-Dist: Click>=7.0
Requires-Dist: click_log>=0.3.2
Requires-Dist: pandas>=1.0.0
Requires-Dist: xlrd>=1.2.0
Provides-Extra: dev
Requires-Dist: black>=23.0.0; extra == "dev"
Requires-Dist: flake8>=6.0.0; extra == "dev"
Requires-Dist: isort>=5.0.0; extra == "dev"
Requires-Dist: mypy>=1.0.0; extra == "dev"
Requires-Dist: pytest>=7.0.0; extra == "dev"
Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
Requires-Dist: tox>=4.0.0; extra == "dev"
Requires-Dist: sphinx>=7.0.0; extra == "dev"
Requires-Dist: sphinx-rtd-theme>=1.0.0; extra == "dev"
Dynamic: license-file

=================
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/github/workflow/status/msk-access/genotype_variants/validate   
        :alt: GitHub Workflow Status

.. 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 <https://github.com/msk-access/GetBaseCountsMultiSample>`_ version 1.2.5 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-samples**: This will run sub-commands `all` for multiple samples 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**

Requires GetBaseCountMultiSample v1.2.5 and above

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
