jacquard 1.1.5
Command-line tools to expedite analysis of Variant Call Format (VCF) files.
License: Apache
Keywords: VCF bioinformatic exome-seq DNA-seq variant-call-format

========
Jacquard
========
Suite of command-line tools to expedite analysis of exome variant data from
multiple patients and multiple variant callers.

.. image:: https://travis-ci.org/umich-brcf-bioinf/Jacquard.svg?branch=develop
    :target: https://travis-ci.org/umich-brcf-bioinf/Jacquard
    :alt: Build Status

.. image:: https://coveralls.io/repos/umich-brcf-bioinf/Jacquard/badge.png?branch=develop
    :target: https://coveralls.io/r/umich-brcf-bioinf/Jacquard?branch=develop
    :alt: Coverage Status

.. image:: https://img.shields.io/pypi/l/Jacquard.svg
    :target: https://pypi.python.org/pypi/jacquard/
    :alt: License

.. image:: http://img.shields.io/pypi/v/colour.svg?style=flat
   :target: https://pypi.python.org/pypi/jacquard/
   :alt: Latest PyPI version


The official repository is at:

https://github.com/umich-brcf-bioinf/Jacquard

Usage
=====

::

   $ jacquard <subcommand> [options] [arguments]

*Subcommands*

:translate:
   Creates new VCFs, adding a controlled vocabulary of new FORMAT tags.
:merge:
   Integrates a directory of VCFs into a single VCF.
:summarize:
   Adds new INFO fields and FORMAT tags that combine variant data from the
   merged VCF.
:expand:
   Explodes a VCF file into a tab-delimited file.

For help on a specific subcommand:

::

   $ jacquard <subcommand> --help


See `ReadTheDocs <http://jacquard.readthedocs.org/>`_ for full documentation.

====

Email bfx-jacquard@umich.edu for support and questions.

UM BRCF Bioinformatics Core


.. _installing-jacquard:

Installing Jaquard
==================
Jacquard has been tested with Python 2.7 and 3.4 on Windows7, OSX, and \*nix.

Prerequisites
-------------
.. note:: Pip installs all required libraries; see [Installing] below.


* natsort (3.5.2)  
* nosetests, testfixtures (3.0.2), and numpy (>=1.7.1) are required for running
  automated tests

Installing
----------
The easiest way to install Jacquard is through PyPI. Get pip if it's
not available in your system:

::

   $ pip install jacquard


You can install from source from github:

::

   $ pip install git+https://github.com/umich-brcf-bioinf/Jacquard


If you don't have root permissions, you can install locally:

::

   $ pip install --user jacquard

.. note:: You may need to modify your path to include the Python install dir
         (e.g. /Users/<username>/.local/bin)



Changelog
=========

1.1.5 (10/26/2020)
------------------
- Adjusted Mutect translate to handle new style tumor/normal sample metaheaders.
- Adjusted Mutect translate to clarify supported versions of Mutect.

1.1.4 (9/29/2020)
-----------------
- Adjusted summarize to ignore phasing when creating consensus GT.
- Adjusted Mutect handling to correctly marked phased normal (0|0)
  as non-somatic.
- Removed extraneous fields from JQ_VS_LOW_CONFIDENCE filter metaheader.

1.1.3 (9/24/2020)
-----------------
- Adjusted Mutect handling to accommodate either older FA or newer AF
  allele frequency tags.

1.1.2 (7/11/2019)
-----------------
- Adjusted VCF handling to correctly pad optional trailing FORMAT fields
- Adjusted Mutect translation to regard PASS as somatic when FilterMutectCalls
  present in metaheaders.

1.1.1 (10/30/2018)
------------------
- Adjusted Mutect translators to:

  - parse normal and tumor designations from SAMPLE metaheaders if available
  - recognize more variations of Mutect metaheader formats

1.1.0 (6/18/2018)
-----------------
- Adjusted *translate* to correctly parse newer versions of Mutect
- Updated supported versions for Mutect, Strelka, Varscan
- Fixed error in JQ_SUMMARY_DP_AVERAGE tag description

1.0.0 (6/5/2018)
-----------------
- Removed obsolete spikes directory
- Fixed bug in *expand* which could overwrite fixed VCF fields (e.g. REF, ALT,
  etc.) if identically named fields in INFO.
- Switched to semantic versioning

0.42 (9/22/2015)
----------------
- Added docs on readthedocs.
- Improved workflow documentation with example data
- *Merge* will now disambiguate tag collisions from multiple VCs
- *Translate*/*summarize* now supports GT tags
- Extended precision to 4 decimal places to support analysis of gene-panels.
- Adjusted translate to handle empty high-confidence VarScan files.

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
- Divya Kriti
- Kevin Meng
- Peter Ulintz