Archive of old versions

These are old versions of GATK and Queue -- for each major version (e.g. 2.4), the last minor version (e.g. 2.4-9) is provided. We make these available for purposes such as comparative testing and project consistency, but you should be aware that these old versions are completely unsupported and that if you choose to use them, you do so at your own risk! If you encounter any bugs in older versions and ask us for help, our only response will be please upgrade to the latest version and see if it still happens because we're not able to put effort into dealing with issues that have already been fixed in later versions. Whenever possible, you should always use the latest and greatest version of GATK and the corresponding version of Queue. Note also that the system requirements for old versions may be different than what is documented for the current version; we do not document these explicitly here but you may find that information in the Version History.

The Tool Documentation for versions going back to 3.5 are available online on the Tool Documentation page through a dropdown menu. To look up arguments and default values for older versions, you will need to use the command-line help system, which you can invoke using --help. You may also want to check the Version History for details of what changed from one version to another.


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.

Important notice

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 to discuss what this means for you.

Source code

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.