Skip to main content
Help improve PyPI by participating in a 5-minute user interface survey!

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.

Build Status Coverage Status License Latest PyPI version

The official repository is at:


$ jacquard <subcommand> [options] [arguments]


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 for full documentation.

Email for support and questions.

UM BRCF Bioinformatics Core

Installing Jaquard

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



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


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


0.42 (X/X/XXXX)

  • 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
  • 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

Release history Release notifications

This version
History Node


History Node


History Node


History Node


Download files

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

Filename, size & hash SHA256 hash help File type Python version Upload date
jacquard-0.42-py2.py3-none-any.whl (56.0 kB) Copy SHA256 hash SHA256 Wheel py2.py3 Sep 22, 2015 (60.2 kB) Copy SHA256 hash SHA256 Source None Sep 22, 2015

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging CloudAMQP CloudAMQP RabbitMQ AWS AWS Cloud computing Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page