This is a pre-production deployment of Warehouse. Changes made here affect the production instance of PyPI (pypi.python.org).
Help us improve Python packaging - Donate today!

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

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

0.42 (X/X/XXXX)

  • 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
Release History

Release History

This version
History Node

0.42

History Node

0.41

History Node

0.40

History Node

0.31

Download Files

Download Files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
jacquard-0.42-py2.py3-none-any.whl (56.0 kB) Copy SHA256 Checksum SHA256 py2.py3 Wheel Sep 22, 2015
jacquard-0.42.zip (60.2 kB) Copy SHA256 Checksum SHA256 Source Sep 22, 2015

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting