Nightlies are the latest versions of GATK to come out of our development pipeline.
They are generated automatically every night and represent the bleeding edge of our work. We provide them for testing bug fixes and so that adventurous souls may experiment with the very latest features, but you should be aware that these versions are completely unsupported, unless we specifically asked you to try them as part of a bug report follow-up. So if you choose to use them, you do so at your own risk. If that's not what you're looking for (and if you're not sure, it probably isn't) you should return to the general Download page and get the latest safe version of GATK.
Be aware also that the nightly builds may have some differences in available arguments and default values relative to the last release, and that the system requirements for nightly build versions may be different than what is documented for the current version.
Docker containers: broadinstitute/gatk-nightly
We do not currently host GATK4 nightlies as file downloads.
All forms of GATK4 are fully open-source under a BSD 3-clause license. Please see the Licensing page for more information.