jacquard 0.40

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:

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

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Email [e-mail] 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