Queue + GATK

Queue is a pipelining system built to work natively with GATK as well as other high-throughput sequence analysis software. Its user documentation is hosted in the GATK forum. Note that the Queue package includes the GATK within the Queue executable, so you do not need to download GATK separately if you plan to run GATK exclusively through Queue.


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.


Queue itself is open-sourced under an MIT license. However, the GATK tools bundled in the Queue package are under a separate license (see Licensing page). If you wish to use Queue without GATK and/or do not meet the terms of the GATK license, we recommend that you build a Queue-only executable from the public GATK framework source.

Source code

The Queue source code is part of the open-source GATK framework. The code is freely available (under MIT license) in the broadgsa/gatk repository on Github.