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https://pypi.python.org/pypi/genotype_variants\n   .. image:: https://img.shields.io/github/actions/workflow/status/msk-access/genotype_variants/validate.yaml\n       :alt: GitHub Actions Workflow Status\n   .. image:: https://readthedocs.org/projects/genotype-variants/badge/?version=develop\n       :target: https://genotype-variants.readthedocs.io/en/latest/?badge=develop\n       :alt: Documentation Status\n   ======  ===========================\n\n\n\nProject to genotype SNV, INDELS and SV.\n\n\n* Free software: Apache Software License 2.0\n* Documentation: https://genotype-variants.readthedocs.io.\n\n\nFeatures\n--------\n\nCurrently this module only supports genotyping and merging small variants (SNV and INDELS).\n\nFor this we have the following command line submodule called **small_variants**. \n\nWhich have the following sub-commands:\n\n* **generate**: To run `GetBaseCountMultiSample \u003chttps://github.com/msk-access/GetBaseCountsMultiSample\u003e`_ version 1.2.5 on given BAM files\n* **merge**: To merge MAF format files w.r.t counts generated from the `generate` command.\n* **all**: This will run both of the sub-commands above `generate` and `merge` togather.\n* **multiple-samples**: This will run sub-commands `all` for multiple samples in the provided metadata file\n\n**Please read the USAGE** (https://genotype-variants.readthedocs.io/en/latest/usage.html) **section of the documentation for more information**\n\nRequires GetBaseCountMultiSample v1.2.5 and above\n\nTo Do\n-----\n\n* Tagging genotyped files for thresholds\n* Genotyping normal buffy coats\n* Genotype structural variants calls\n\n\nCredits\n-------\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: 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