Skip to main content

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

Project description

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

.. image::
:alt: Build Status

.. image::
:alt: Coverage Status

.. image::
:alt: License

.. image::
:alt: Latest PyPI version

The official repository is at:



$ jacquard <subcommand> [options] [arguments]


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

For help on a specific subcommand:


$ jacquard <subcommand> --help

See `ReadTheDocs <>`_ for full documentation.


Email 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.

.. 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

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+

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)


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:


- 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

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distributions

No source distribution files available for this release.See tutorial on generating distribution archives.

Built Distribution

jacquard-1.1.1-py3-none-any.whl (57.5 kB view hashes)

Uploaded Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page