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        "author": "University of Michigan Bioinformatics Core",
        "author_email": "bfx-jacquard@umich.edu",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Environment :: Console",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "========\nJacquard\n========\nSuite of command-line tools to expedite analysis of exome variant data from\nmultiple patients and multiple variant callers.\n\n.. image:: https://travis-ci.org/umich-brcf-bioinf/Jacquard.svg?branch=develop\n    :target: https://travis-ci.org/umich-brcf-bioinf/Jacquard\n    :alt: Build Status\n\n.. image:: https://coveralls.io/repos/umich-brcf-bioinf/Jacquard/badge.png?branch=develop\n    :target: https://coveralls.io/r/umich-brcf-bioinf/Jacquard?branch=develop\n    :alt: Coverage Status\n\n.. image:: https://img.shields.io/pypi/l/Jacquard.svg\n    :target: https://pypi.python.org/pypi/jacquard/\n    :alt: License\n\n.. image:: http://img.shields.io/pypi/v/colour.svg?style=flat\n   :target: https://pypi.python.org/pypi/jacquard/\n   :alt: Latest PyPI version\n\n\nThe official repository is at:\n\nhttps://github.com/umich-brcf-bioinf/Jacquard\n\nUsage\n=====\n\n::\n\n   $ jacquard <subcommand> [options] [arguments]\n\n*Subcommands*\n\n:translate:\n   Creates new VCFs, adding a controlled vocabulary of new FORMAT tags.\n:merge:\n   Integrates a directory of VCFs into a single VCF.\n:summarize:\n   Adds new INFO fields and FORMAT tags that combine variant data from the\n   merged VCF.\n:expand:\n   Explodes a VCF file into a tab-delimited file.\n\nFor help on a specific subcommand:\n\n::\n\n   $ jacquard <subcommand> --help\n\n\nSee `ReadTheDocs <http://jacquard.readthedocs.org/>`_ for full documentation.\n\n====\n\nEmail bfx-jacquard@umich.edu for support and questions.\n\nUM BRCF Bioinformatics Core\n\n\n.. _installing-jacquard:\n\nInstalling Jaquard\n==================\nJacquard has been tested with Python 2.7 and 3.4 on Windows7, OSX, and \\*nix.\n\nPrerequisites\n-------------\n.. note:: Pip installs all required libraries; see [Installing] below.\n\n\n* natsort (3.5.2)  \n* nosetests, testfixtures (3.0.2), and numpy (>=1.7.1) are required for running\n  automated tests\n\nInstalling\n----------\nThe easiest way to install Jacquard is through PyPI. Get pip if it's\nnot available in your system:\n\n::\n\n   $ pip install jacquard\n\n\nYou can install from source from github:\n\n::\n\n   $ pip install git+https://github.com/umich-brcf-bioinf/Jacquard\n\n\nIf you don't have root permissions, you can install locally:\n\n::\n\n   $ pip install --user jacquard\n\n.. note:: You may need to modify your path to include the Python install dir\n         (e.g. /Users/<username>/.local/bin)\n\n\n\nChangelog\n=========\n\n1.1.2 (7/11/2019)\n-----------------\n- Adjusted VCF handling to correctly pad optional trailing FORMAT fields\n- Adjusted Mutect translation to regard PASS as somatic when FilterMutectCalls\n  present in metaheaders.\n\n1.1.1 (10/30/2018)\n------------------\n- Adjusted Mutect translators to:\n\n  - parse normal and tumor designations from SAMPLE metaheaders if available\n  - recognize more variations of Mutect metaheader formats\n\n1.1.0 (6/18/2018)\n-----------------\n- Adjusted *translate* to correctly parse newer versions of Mutect\n- Updated supported versions for Mutect, Strelka, Varscan\n- Fixed error in JQ_SUMMARY_DP_AVERAGE tag description\n\n1.0.0 (6/5/2018)\n-----------------\n- Removed obsolete spikes directory\n- Fixed bug in *expand* which could overwrite fixed VCF fields (e.g. REF, ALT,\n  etc.) if identically named fields in INFO.\n- Switched to semantic versioning\n\n0.42 (9/22/2015)\n----------------\n- Added docs on readthedocs.\n- Improved workflow documentation with example data\n- *Merge* will now disambiguate tag collisions from multiple VCs\n- *Translate*/*summarize* now supports GT tags\n- Extended precision to 4 decimal places to support analysis of gene-panels.\n- Adjusted translate to handle empty high-confidence VarScan files.\n\n0.41 (5/7/2015)\n---------------\n - Combined *filter* command with *merge* command\n - Extended *expand* to create simple metaheader glossary\n - Adjusted code to support Python >=2.7 or 3.x\n - Improved checks for consistent VCF file sets\n - Fixed bug in *merge* that caused error if any VCFs were unsorted\n - Fixed bug in *summarize* that caused error if variant was called by subset\n   of callers\n\n0.31 (3/17/2015)\n----------------\n - Downgraded VCF format from 4.2 to 4.1\n - Fixed a bug that omitted CALLERS_REPORTED_LIST summary tag\n - Simplified summary tags; removed dependency on numpy\n - Adjusted VarScan translation to accept a file pattern to identify\n   high-confidence files\n\n\n0.3 (3/9/2015)\n--------------\n - Replaced *normalize*, *tag* commands with *translate*; relaxed constraints\n   on incoming data.\n - Renamed *consensus* to *summarize*\n - More consistent behavior in *expand*\n - Significantly improved *merge* performance\n - Added new summary tags:\n\n   - CALLERS_REPORTED_COUNT\n   - CALLERS_REPORTED_LIST\n   - SAMPLES_REPORTED_COUNT\n   - CALLERS_PASSED_COUNT\n   - CALLERS_PASSED_LIST\n   - SAMPLES_PASSED_COUNT\n\n - Fixed bug in how Strelka calculated AF on indels\n - Improved command validation and error handling\n - Added project/code documentation\n - Removed dependencies on pandas\n\n\n0.21 (10/2014)\n--------------\n - Initial public release\n\n\nJacquard is written and maintained by the University of Michigan \nBRCF Bioinformatic Core; individual contributors include:\n\n- Jessica Bene\n- Ashwini Bhasi\n- Chris Gates\n- Divya Kriti\n- Kevin Meng\n- Peter Ulintz\n\n",
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