Metadata-Version: 2.0
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
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
Requires-Dist: natsort

========
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

