gatk-tools: Utilities for processing sequencing data and genomic variants using GATK

This package contains some utilities for processing sequencing data and genomic variants using the framework provided by the Genome Analysis Toolkit (GATK).

Installing and running gatk-tools

Please see README file for more information on the utilities available within the package and details of how to install and run the tools from a pre-packaged release.

For more information on the utilities available in this package, and how to install and run these tools, please see the README file.

Building from source

The gatk-tools package is built using Apache Maven, a software project management and build automation tool. Details on how to install and run Maven can be found here.

Maven will automatically download dependencies from the central Maven repository with the exception of the GATK library. GATK is available under a dual licensing model with separate licenses for academic, non-commerical research and for-profit purposes, and can be downloaded from the GATK site. The GATK JAR file will need to be installed separately as shown in the following instructions.

1. Clone the project

    git clone https://github.com/crukci-bioinformatics/gatk-tools.git
    cd gatk-tools
   

2. Install the GATK jar file to the local Maven repository (substituting the version and path to the GATK jar as appropriate)

    mvn install:install-file -Dpackaging=jar -DgroupId=org.broadinstitute.gatk -DartifactId=gatk -Dversion=3.8 -Dfile=GenomeAnalysisTK.jar
   

3. Build and package the gatk-tools package

    mvn package
   

4. Unpack the gatk-tools tarball to an installation directory (substituting the version number as appropriate)

    tar zxf target/gatk-tools-1.0-distribution.tar.gz
   

This will create a directory named gatk-tools-1.0 which can be moved to the desired installation location.