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.
The official repository is at:
https://github.com/umich-brcf-bioinf/Jacquard
Files
jacquard-runner.py : Convenience wrapper for running Jacquard directly from source tree.
jacquard : Python libraries
spikes : Unsupported prototypes and other experiments
test : Automated unit tests
Usage
$jacquard <subcommand> [options] [arguments]
Subcommands
- translate:
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.
- merge:
Accepts a directory of VCFs and returns a single merged VCF file. Optionally filters to a subset of variants/loci.
- summarize:
Accepts a Jacquard-merged VCF file and creates a new VCF file, adding summary fields/tags.
- expand:
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 bfx-jacquard@umich.edu for support and questions.
UM BRCF Bioinformatics Core
Changelog
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
Added new summary tags: - CALLERS_REPORTED_COUNT - CALLERS_REPORTED_LIST - SAMPLES_REPORTED_COUNT - CALLERS_PASSED_COUNT - CALLERS_PASSED_LIST - SAMPLES_PASSED_COUNT
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