The GATK package download includes all released GATK tools. Please see Getting Started for a quick start primer on using GATK, and see the Version History for release notes and highlights of differences between versions. You will need to be registered and logged into the GATK forum to access the download.
All POSIX operating systems (Unix, Linux, MacOSX etc) are supported. Microsoft Windows is not supported. The current version requires Java 1.8. Note that the Oracle Java is preferred; OpenJDK is not officially supported.
The GATK package is made available for free to academic researchers under a limited license for non-commercial use. If you plan to use the GATK for-profit, you will need to purchase a license. Please see the Licensing page for more information.
We have open-sourced the upcoming new version, GATK4, which is available today as Beta release and will be released into General Availability status in an August-September 2017 timeframe. See the GATK blog for a detailed announcement. This page will be updated to reflect the new licensing policy when GATK 4.0 is released into General Availability.
If you are currently holding a commercial license for the current version or an older version of GATK, please contact firstname.lastname@example.org to discuss what this means for you.
The source code for the full GATK package is available in the broadgsa/gatk-protected repository on Github. The source code for the GATK engine, which is open-source, is also available separately in the broadgsa/gatk repository on Github. This includes the engine, infrastructure libraries, Queue and many utility tools. It is intended for developers who wish to develop their own tools, and is freely available to all under the MIT license.
Recent versions of GATK 3.x are available in the broadinstitute/gatk3 repository on Dockerhub.