The GATK download includes all released GATK tools for error modeling, data compression, and variant calling. Queue is a pipelining system built to work natively with GATK as well as other high-throughput sequence analysis software (the Queue package includes the GATK within the Queue.jar binary). To obtain the source code, follow the link below to our online Github repository, where you will have the option to either download the codebase as an archive package or to clone the Git repository.
Please be aware that this is cutting-edge research software, with the downsides that this implies. Some parts of the GATK tool chain are under active development, and you may occasionally run into bugs that we haven't caught yet. Rest assured we are working hard to make these tools faster, more stable, and more scalable all the time -- and be sure to update your version regularly to benefit from the latest bug fixes and improvements!
If you plan to use the GATK for-profit, you will need to purchase a license through our commercial partner, Appistry. Please see the Appistry-GATK website for more information. GATK-Lite is no longer available as of version 2.4; see this blog post for more details of the relevant changes.
The programming framework includes the engine, infrastructure libraries 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. To obtain the source code of the programming framework, follow the link below to our online Github repository, where you will have the option to either download the codebase as an archive package or to clone the Git repository.
The GATK resource bundle is a collection of standard files for working with human resequencing data with the GATK. Please see this article for further details on the content of this resource bundle. The bundle is available for download from our public FTP server.
MuTect is a GATK-based variant caller specialized for somatic/cancer variants developed by our collaborators from the Cancer Genome Analysis program here at Broad. Please see the MuTect forum for documentation and support.