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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:


  • : Convenience wrapper for running Jacquard directly from source tree.

  • jacquard : Python libraries

  • spikes : Unsupported prototypes and other experiments

  • test : Automated unit tests


$jacquard <subcommand> [options] [arguments]



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.


Accepts a directory of VCFs and returns a single merged VCF file. Optionally filters to a subset of variants/loci.


Accepts a Jacquard-merged VCF file and creates a new VCF file, adding summary fields/tags.


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 for support and questions.

UM BRCF Bioinformatics Core


0.40 (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

  • Kevin Meng

  • Peter Ulintz

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