The code for GATK versions 4.x is in a publicly accessible Github repository:
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.
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.
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.
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.
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@example.com) to inquire about licensing terms. Or you could do us all a favor and just switch to GATK4 which is fully open-source :)