{ "info": { "author": "Steve Davis", "author_email": "steven.davis@fda.hhs.gov", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: Freely Distributable", "Natural Language :: English", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "===============================\nVCF Toolz\n===============================\n\n\n.. Image showing the PyPI version badge - links to PyPI\n.. image:: https://img.shields.io/pypi/v/vcftoolz.svg\n :target: https://pypi.python.org/pypi/vcftoolz\n\n.. Image showing the Travis Continuous Integration test status, commented out for now\n.. .. image:: https://img.shields.io/travis/CFSAN-Biostatistics/vcftoolz.svg\n.. :target: https://travis-ci.org/CFSAN-Biostatistics/vcftoolz\n\n.. Image showing the JOSS paper badge\n.. image:: http://joss.theoj.org/papers/10.21105/joss.01144/status.svg\n :target: https://doi.org/10.21105/joss.01144\n\nTools for working with Variant Call Format files.\n\nVCF Toolz was developed by the United States Food\nand Drug Administration, Center for Food Safety and Applied Nutrition.\n\n* Free software\n* Documentation: https://vcftoolz.readthedocs.io\n* Source Code: https://github.com/CFSAN-Biostatistics/vcftoolz\n* PyPI Distribution: https://pypi.python.org/pypi/vcftoolz\n\n\nFeatures\n--------\n\n* Compares the snps in two or more VCF files.\n* Lists the snps that are unique to each VCF file with full genotype information per snp.\n* Lists the snps that are missing from each VCF file if present in at least two other VCF files.\n* Generates Venn diagrams of positions and snps in the VCF files.\n* Reports precision, recall, and F1 score when the truth is known.\n* Reports the effectiveness of filtered variants when the truth is known.\n* Reformat the VCF file in a tall-narrow format for easy viewing and diffs.\n* Count samples, positions, calls, snps, indels, other variants, missing calls, and filter reasons.\n* Plot calls along the length of the genome and show the location of filtered calls.\n\n\nCiting VCF Toolz\n--------------------------------------\n\nTo cite VCF Toolz, please reference the VCF Toolz paper:\n\n https://doi.org/10.21105/joss.01144\n\n\nLicense\n-------\n\nSee the LICENSE file included in the VCF Toolz distribution.\n\n\n\n\n\nHistory\n=======\n\n1.2.0 (2019-04-04)\n---------------------\n* Fix defect in narrow command wrongly printing ALT=. when GT=.\n* Add the ``count`` command to count samples, positions, calls, snps, indels,\n other variants, filtered calls, missing calls, and filter reasons.\n* Add the ``plot`` command to plot calls along the length of the genome and show\n the location of filtered calls.\n* Change the text of the compare report to refer to \"Calls\", not \"Sample snps\".\n* Drop support for Python 3.4, which is not supported by matplotlib.\n* Add support for Python 3.7.\n\n1.1.1 (2019-03-26)\n---------------------\n* Replace None with '.' when printing call data.\n* Support VCF files with multiple alternate alleles per position.\n\n1.1.0 (2019-02-06)\n---------------------\n* Support reading gzip compressed vcf files.\n\n\n1.0.0 (2018-11-20)\n---------------------\n\n* First public release.\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/CFSAN-Biostatistics/vcftoolz", "keywords": "bioinformatics", "license": "BSD", "maintainer": "", "maintainer_email": "", "name": "vcftoolz", "package_url": "https://pypi.org/project/vcftoolz/", "platform": "", "project_url": "https://pypi.org/project/vcftoolz/", "project_urls": { "Homepage": "https://github.com/CFSAN-Biostatistics/vcftoolz" }, "release_url": 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