jacquard 1.1.1

Command-line tools to expedite analysis of Variant Call Format (VCF) files.

========
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

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 [e-mail] 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
=========

1.1.1 (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