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]
|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 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.
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+https://github.com/umich-brcf-bioinf/Jacquard
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)
- 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:
- Jessica Bene
- Ashwini Bhasi
- Chris Gates
- Divya Kriti
- Kevin Meng
- Peter Ulintz
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