{ "info": { "author": "University of Michigan Bioinformatics Core", "author_email": "bfx-zither@umich.edu", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Environment :: Console", "Intended Audience :: Science/Research", "License :: OSI Approved :: Apache Software License", "Operating System :: Unix", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "====== \nZither\n======\n\nCommand-line tool to pull raw depths and alt freqs from BAM file(s) based on an existing VCF, writing output as new VCF to stdout.\n\n.. image:: https://travis-ci.org/umich-brcf-bioinf/Zither.svg?branch=develop\n :target: https://travis-ci.org/umich-brcf-bioinf/Zither\n :alt: Build Status\n\n.. image:: https://coveralls.io/repos/umich-brcf-bioinf/zither/badge.svg?branch=develop&service=github\n :target: https://coveralls.io/github/umich-brcf-bioinf/zither?branch=develop\n :alt: Coverage Status\n\n\n\nThe official repository is at:\n\nhttps://github.com/umich-brcf-bioinf/Zither\n\n----------\nQuickstart\n----------\n\nRead a single BAM file\n======================\n\n $ zither --bam examples/explicit_bam/Sample_X.bam examples/explicit_bam/input.vcf > output.vcf \n\nGiven a VCF and a BAM file, read positions in the input VCF and corresponding pileups \nfrom Sample_X.bam.\n\n\nRead a set of matched VCF sample names and BAM files\n====================================================\n\n $ zither examples/matching_names/input.vcf > output.vcf \n\nGiven a VCF and a collection of BAM files whose file names \nmatch the VCF sample names, reads positions from the \ninput VCF and corresponding BAM pileups.\n\n\nExplicitly map VCF sample names to BAM files\n====================================================\n\n $ zither --mapping_file=examples/mapping_files/mapping_file.txt examples/mapping_files/input.vcf > output.vcf \n\nGiven a VCF, a collection of BAMs, and a file that maps sample names to BAM paths,\nreads positions from the input VCF and corresponding pileups \nfrom BAM files names. \n\nThe mapping file is a tab-separated text file where each line has a sample \nname and the path to the corresponding BAM file. Paths to BAM files can be \nabsolute or relative; relative paths are resolved relative to the directory \nthat contains the mapping file. \n\n====\n\nEmail bfx-zither@umich.edu for support and questions.\n\nUM BRCF Bioinformatics Core \n\n\nChangelog\n=========\n\n0.2 (9/3/2015)\n--------------\n- Adjusted tags to include total and unfiltered depth and alt freq.\n- Added basecall quality filtering\n- Added depth cutoff\n- Added support for Python3\n\n0.1 (8/6/2015)\n--------------\nInitial Release\n\nZither is written and maintained by the University of Michigan \nBRCF Bioinformatic Core; individual contributors include:\n\n- Chris Gates\n- Divya Kriti", "description_content_type": null, "docs_url": null, "download_url": "UNKNOWN", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/umich-brcf-bioinf/Zither", "keywords": "VCF bioinformatic exome-seq DNA-seq variant-call-format BAM", "license": "Apache", "maintainer": null, "maintainer_email": null, "name": "zither", "package_url": "https://pypi.org/project/zither/", "platform": "UNKNOWN", "project_url": "https://pypi.org/project/zither/", "project_urls": { "Download": "UNKNOWN", "Homepage": "https://github.com/umich-brcf-bioinf/Zither" }, "release_url": "https://pypi.org/project/zither/0.2/", "requires_dist": null, "requires_python": null, "summary": "Command-line tool to pull raw depths and alt freqs from BAM file(s) based on an existing VCF, writing output as new VCF to stdout.", "version": "0.2" }, "last_serial": 1706382, "releases": { "0.2": [ { "comment_text": "", "digests": { "md5": "eb1f3667dc56d1ae5ac264c4f8d6bebe", "sha256": "1bca324825a3f9d69a0645f9977665f4b6670d0149525d511359b1267c91b214" }, "downloads": -1, "filename": "zither-0.2-py2-none-any.whl", "has_sig": false, "md5_digest": "eb1f3667dc56d1ae5ac264c4f8d6bebe", "packagetype": "bdist_wheel", "python_version": "py2", "requires_python": null, "size": 9391, "upload_time": "2015-09-03T13:22:29", "url": "https://files.pythonhosted.org/packages/b8/a4/822943e28171313b6d6bc4c7bc20b5f5f4744725c0d561f91de0838a308d/zither-0.2-py2-none-any.whl" }, { "comment_text": "", "digests": { "md5": "6263b1c32cb4f06c790617ec714180a4", "sha256": "a998f6f330a70f10a99789619445bdc834314588bf3619d1e5fd0a72d2a6dd32" }, "downloads": -1, "filename": "zither-0.2.tar.gz", "has_sig": false, "md5_digest": "6263b1c32cb4f06c790617ec714180a4", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 7477, "upload_time": "2015-09-03T13:22:33", "url": "https://files.pythonhosted.org/packages/81/3a/1983b665386510955ea6f64bdf556c7d05d8a94e7708a432b0c0e8d2010f/zither-0.2.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "eb1f3667dc56d1ae5ac264c4f8d6bebe", "sha256": "1bca324825a3f9d69a0645f9977665f4b6670d0149525d511359b1267c91b214" }, "downloads": -1, "filename": "zither-0.2-py2-none-any.whl", "has_sig": false, "md5_digest": "eb1f3667dc56d1ae5ac264c4f8d6bebe", "packagetype": "bdist_wheel", "python_version": "py2", "requires_python": null, "size": 9391, "upload_time": "2015-09-03T13:22:29", "url": "https://files.pythonhosted.org/packages/b8/a4/822943e28171313b6d6bc4c7bc20b5f5f4744725c0d561f91de0838a308d/zither-0.2-py2-none-any.whl" }, { "comment_text": "", "digests": { "md5": "6263b1c32cb4f06c790617ec714180a4", "sha256": "a998f6f330a70f10a99789619445bdc834314588bf3619d1e5fd0a72d2a6dd32" }, "downloads": -1, "filename": "zither-0.2.tar.gz", "has_sig": false, "md5_digest": "6263b1c32cb4f06c790617ec714180a4", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 7477, "upload_time": "2015-09-03T13:22:33", "url": "https://files.pythonhosted.org/packages/81/3a/1983b665386510955ea6f64bdf556c7d05d8a94e7708a432b0c0e8d2010f/zither-0.2.tar.gz" } ] }