Where can I get the GATK source code
IMPORTANT: This is the legacy GATK documentation. This information is only valid until Dec 31st 2019. For latest documentation and forum click here
created by Geraldine_VdAuwera
on 2014-04-04
We distinguish "Classic GATK" (major versions 1 through 3) and GATK 4, the next generation of GATK tools.
"Classic GATK" (major versions 1 through 3) (current distribution)
We provide the current GATK source code through two publicly accessible Github repositories: broadgsa/gatk and broadgsa/gatk-protected.
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.
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 (softwarelicensing@broadinstitute.org) to inquire about licensing terms.
GATK 4+
The code for GATK 4+, currently available as an alpha preview, is accessible through two publicly accessible Github repositories: broadinstitute/gatk and broadinstitute/gatk-protected. The division is also based on having two different licenses, like Classic GATK, but in this case the repositories are complementary; there is no code shared between them.
This repository contains the code corresponding to the core GATK 4+ development framework, including the new GATK engine and many utilities, which third-party developers can use to develop their own GATK-based analysis tools. We encourage developers to use this new framework for development and we welcome feedback regarding features and development support.
All the code in this repository is open-source under a BSD license. The full text of the license can be viewed here.
This repository contains the code for key analysis tools that are covered 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 (softwarelicensing@broadinstitute.org) to inquire about licensing terms.
Updated on 2015-12-19
From YingLiu on 2017-04-24
how to build gatk-protected code to generate a gatk.jar file ??
From Geraldine_VdAuwera on 2017-04-24
You run the build command
mvn verify
There are also options to make it go faster here: http://gatkforums.broadinstitute.org/gatk/discussion/5784/howto-speed-up-gatk-compilation