https://github.com/msk-access/genotype_variants

Project to genotype SNV, INDEL and SV.
https://github.com/msk-access/genotype_variants

genotyping msk-access

Last synced: 4 months ago
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Project to genotype SNV, INDEL and SV.

• Host: GitHub
• URL: https://github.com/msk-access/genotype_variants
• Owner: msk-access
• License: other
• Created: 2020-01-30T06:19:57.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2025-09-29T16:03:02.000Z (8 months ago)
• Last Synced: 2025-09-29T17:36:42.198Z (8 months ago)
• Topics: genotyping, msk-access
• Language: Python
• Homepage: https://genotype-variants.rtfd.io
• Size: 210 KB
• Stars: 1
• Watchers: 1
• Forks: 4
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst
  • Changelog: HISTORY.rst
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE
  • Authors: AUTHORS.rst

Awesome Lists containing this project

README

          
=================

genotype_variants

=================

.. table:: Badges

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   Badge   Link

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   .. image:: https://img.shields.io/pypi/v/genotype_variants.svg

       :target: https://pypi.python.org/pypi/genotype_variants

   .. image:: https://img.shields.io/github/actions/workflow/status/msk-access/genotype_variants/validate.yaml

       :alt: GitHub Actions Workflow Status

   .. image:: https://readthedocs.org/projects/genotype-variants/badge/?version=develop

       :target: https://genotype-variants.readthedocs.io/en/latest/?badge=develop

       :alt: Documentation Status

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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 `_ 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