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We provide the GATK source code through two publicly accessible Github repositories: broadgsa/gatk and broadgsa/gatk-protected. This document explains what are the differences between the two and, importantly, what software licenses cover their contents.

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. All the code in this repository is open-source under the MIT license.

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 which prohibits for-profit use. Anyone interested in accessing the protected code for for-profit purposes should contact our commercial partner, Appistry, to inquire about licensing terms.

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