GATK 4 will be the next major version of GATK, bringing together well-established tools from the GATK and Picard codebases under a single simplified, streamlined framework, and enabling selected tools to be run in a massively parallel way on local clusters or in the cloud using Apache Spark. This package contains the latest Beta release.
This project is in a beta development stage, which means it is not yet ready for general use, documentation is absent or incomplete, and that some features and syntax may still change substantially before general release. Be sure to read about the known issues before test driving. See the GATK4 Beta Quickstart doc to get started and the README for details. Some additional documentation can currently be found in the GATK 4 Alpha forum and in the source code repository.
All POSIX operating systems (Unix, Linux, MacOSX etc) are supported. Microsoft Windows is not supported. The current version requires Java 8. Note that the Oracle Java is preferred; OpenJDK is not officially supported. A few tools require R 3.1.3 (mainly for plotting). An Rscript is available here to install any R libraries not already present on your system. This Rscript can be invoked as follows:
Rscript install_R_packages.R. There is a frontend launching script provided for convenience that requires Python version 2.6 or greater.
The GATK 4 Beta package is open source under a BSD (3-clause) license.
The source code for GATK 4.x is available in the broadinstitute/gatk repository on Github.
Starting with the Beta release, docker images of all GATK4 versions are available in the Dockerhub at broadinstitute/gatk repository on Dockerhub.