Metadata-Version: 1.1
Name: jacquard
Version: 0.41
Summary: Command-line tools to expedite analysis of Variant Call Format (VCF) files.
Home-page: https://github.com/umich-brcf-bioinf/Jacquard
Author: University of Michigan Bioinformatics Core
Author-email: bfx-jacquard@umich.edu
License: Apache
Description: ========
        Jacquard
        ========
        Suite of command-line tools to expedite analysis of exome variant data from 
        multiple patients and multiple variant callers.
        
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        The official repository is at:
        
        https://github.com/umich-brcf-bioinf/Jacquard
        
        Files
        =====
        - jacquard-runner.py : Convenience wrapper for running Jacquard directly from source tree.
        - jacquard : Python libraries
        - spikes : Unsupported prototypes and other experiments
        - test : Automated unit tests
        
        Usage
        =====
        ``$jacquard <subcommand> [options] [arguments]``
        
        *Subcommands*
        
        :translate:
           Accepts a directory of VCF results (including VarScan high confidence 
           files). Creates a new directory of VCFs, adding Jacquard-specific FORMAT 
           tags for each VCF record.
        :merge:
           Accepts a directory of VCFs and returns a single merged VCF file.
           Optionally filters to a subset of variants/loci.
        :summarize:
           Accepts a Jacquard-merged VCF file and creates a new VCF file, adding 
           summary fields/tags.
        :expand:
           Transforms VCF file into tab-separated text file expanding INFO fields and 
           FORMAT tags into discrete columns.
        
        For help on a specific subcommand:
        
        ``jacquard <subcommand> --help``
        
        ====
        
        Email bfx-jacquard@umich.edu for support and questions.
        
        UM BRCF Bioinformatics Core
        
        
        
        Changelog
        =========
        
        0.41 (5/7/2015)
        ---------------
         - Combined filter command with merge command
         - Extended expand to create simple metaheader glossary
         - Adjusted code to support Python >=2.7 or 3.x
         - Improved checks for consistent VCF file sets
         - Fixed bug in merge that caused error if any VCFs were unsorted
         - Fixed bug in summarize that caused error if variant was called by subset of callers 
        
        0.31 (3/17/2015)
        ----------------
         - Downgraded VCF format from 4.2 to 4.1
         - Fixed a bug that omitted CALLERS_REPORTED_LIST summary tag
         - Simplified summary tags; removed dependency on numpy
         - Adjusted VarScan translation to accept a file pattern to identify high-confidence files 
        
        
        0.3 (3/9/2015)
        --------------
         - Replaced [normalize], [tag] commands with [translate]; relaxed constraints on incoming data.
         - Renamed [consensus] to [summarize]
         - More consistent behavior in [expand]
         - Significantly improved [merge] performance 
         - Added new summary tags:
           - CALLERS_REPORTED_COUNT
           - CALLERS_REPORTED_LIST
           - SAMPLES_REPORTED_COUNT
           - CALLERS_PASSED_COUNT
           - CALLERS_PASSED_LIST
           - SAMPLES_PASSED_COUNT
         - Fixed bug in how Strelka calculated AF on indels
         - Improved command validation and error handling
         - Added project/code documentation 
         - Removed dependencies on pandas
          
          
        0.21 (10/2014)
        --------------
         - Initial public release
        
        
        
        
        Jacquard is written and maintained by the University of Michigan 
        BRCF Bioinformatic Core; individual contributors include:
        
        - Jessica Bene
        - Ashwini Bhasi
        - Chris Gates
        - Kevin Meng
        - Peter Ulintz
Keywords: VCF bioinformatic exome-seq DNA-seq variant-call-format
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
