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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:

https://github.com/umich-brcf-bioinf/Jacquard

Usage

$ jacquard <subcommand> [options] [arguments]

Subcommands

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 bfx-jacquard@umich.edu for support and questions.

UM BRCF Bioinformatics Core

Installing Jaquard

Jacquard has been tested with Python 2.7 and 3.4 on Windows7, OSX, and *nix.

Prerequisites

Note

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

Installing

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

Note

You may need to modify your path to include the Python install dir (e.g. /Users/<username>/.local/bin)

Changelog

1.1.5 (10/26/2020)

  • Adjusted Mutect translate to handle new style tumor/normal sample metaheaders.
  • Adjusted Mutect translate to clarify supported versions of Mutect.

1.1.4 (9/29/2020)

  • 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.

1.1.3 (9/24/2020)

  • Adjusted Mutect handling to accommodate either older FA or newer AF allele frequency tags.

1.1.2 (7/11/2019)

  • Adjusted VCF handling to correctly pad optional trailing FORMAT fields
  • Adjusted Mutect translation to regard PASS as somatic when FilterMutectCalls present in metaheaders.

1.1.1 (10/30/2018)

  • Adjusted Mutect translators to:
    • parse normal and tumor designations from SAMPLE metaheaders if available
    • recognize more variations of Mutect metaheader formats

1.1.0 (6/18/2018)

  • 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

1.0.0 (6/5/2018)

  • 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

0.42 (9/22/2015)

  • 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.

0.41 (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
  • Divya Kriti
  • Kevin Meng
  • Peter Ulintz

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