Command-line tools to expedite analysis of Variant Call Format (VCF) files.
Suite of command-line tools to expedite analysis of exome variant data from multiple patients and multiple variant callers.
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 email@example.com for support and questions.
UM BRCF Bioinformatics Core
Jacquard has been tested with Python 2.7 and 3.4 on Windows7, OSX, and *nix.
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+https://github.com/umich-brcf-bioinf/Jacquard
If you don’t have root permissions, you can install locally:
$ pip install --user jacquard
Adjusted Mutect translate to handle new style tumor/normal sample metaheaders.
Adjusted Mutect translate to clarify supported versions of Mutect.
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.
Adjusted Mutect handling to accommodate either older FA or newer AF allele frequency tags.
Adjusted VCF handling to correctly pad optional trailing FORMAT fields
Adjusted Mutect translation to regard PASS as somatic when FilterMutectCalls present in metaheaders.
Adjusted Mutect translators to:
parse normal and tumor designations from SAMPLE metaheaders if available
recognize more variations of Mutect metaheader formats
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
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
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.
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
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
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
Initial public release
Jacquard is written and maintained by the University of Michigan BRCF Bioinformatic Core; individual contributors include:
Release history Release notifications | RSS feed
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.