Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Where can I get the GATK source code? Is it open-source?

YES! Starting with GATK4 it is fully open-source under a BSD 3-clause license.

The code for GATK versions 4.x is in a publicly accessible Github repository:

broadinstitute/gatk

This repository contains the code corresponding to the core GATK 4+ development framework, including the new GATK engine and many utilities in addition to the GATK analysis tools themselves. We encourage third-party developers to use this new framework for development, and we welcome feedback regarding features and development support requests.

All the code in this repository is open-source under a BSD license. The full text of the license can be viewed here.

You may also be interested in the gatk-workflows family of repositories, where we publish our workflow scripts for public consumption, as well as the GATK Docker repository, where we publish docker containers of all new released versions of GATK.


Legacy GATK code

Also known as "Classic GATK", this covers major versions 1 through 3. We provide the old GATK source code through two publicly accessible Github repositories: broadgsa/gatk and broadgsa/gatk-protected. There is also a GATK3 Docker repository that contains docker containers for the 3.x series.

1. broadgsa/gatk

This repository contains the code corresponding to the core GATK development framework, including the GATK engine and many utilities, which third-party developers can use to develop their own GATK-based analysis tools. Be advised however that support for development using this framework is being discontinued.

All the code in this repository is open-source under the MIT license. The full text of the license can be viewed here.

2. broadgsa/gatk-protected

This repository contains the code corresponding to the GenomeAnalysisTK.jar file that we distribute to our users, containing the GATK engine and all analysis tools.

This includes the code in broadgsa/gatk under the MIT license, plus tools and utilities that are under a more restrictive license that prohibits commercial/for-profit use. Anyone interested in accessing the protected code for commercial/for-profit purposes should contact our licensing department ([email protected]) to inquire about licensing terms. Or you could do us all a favor and just switch to GATK4 which is fully open-source :)

Post edited by Sheila on
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