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. 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.
Queue was a pipelining system built to work natively with GATK as well as other high-throughput sequence analysis software. The GATK itself is bundled within the Queue executable, so you do not need to download GATK separately if you plan to run GATK exclusively through Queue.
Queue has been replaced by Cromwell+WDL, a more general and powerful pipelining solution.
Mutect 1 was a somatic SNV caller built on top of GATK but distributed as a standalone tool, originally developed by our collaborators from the Cancer Genome Analysis program at the Broad Institute. This tool was limited to calling SNVs.
This tool has been replaced by Mutect2, a much improved somatic SNV and indel caller included in GATK4.
These packages are made available for free to academic researchers under a limited license for non-commercial use. If you need to use one of these packages for commercial use, please contact email@example.com to discuss what arrangements can be made.
For GATK and Queue, we provide the last minor version (e.g. 2.4-9) for each major version (e.g. 2.4). If you need a different minor version, you will need to build it from source.
The GATK Tool Documentation pages 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.