Please see the Version History page for information on the latest changes and full release notes.
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GATK 2 includes all of the original GATK 1.x tools as well as many newer and more advanced tools for error modeling, data compression, and variant calling. The version of Queue provided below is built for GATK 2. 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 2 tool chain are still under heavy development, and you may experience some issues with speed, stability and scalability. However, these tools provide radically improved calling sensitivity, specificity and performance, so are worth the exposure even though the software isn't quite mature 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 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 announcement for more details of the recent 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.