GATK4-Protected (codename Hellbender-protected)

GATK4 development of the license-protected part of the toolkit

This README is aimed at developers. For user information, please see the GATK 4 forum

Requirements

• R 3.1.3 see additional requirements below: R package requirements

• Java 8

• (Developers) Gradle 2.13 is needed for building the GATK. We recommend using the ./gradlew script which will download and use an appropriate gradle version automatically.

• (Developers) git lfs 1.1.0 (or greater) is needed for testing GATK-Protected builds. It is needed to download large files for the complete test suite. Run git lfs install after downloading, followed by git lfs pull to download the large files. The download is ~500 MB.

Read GATK 4 README

Please refer to the GATK 4 public repo readme file for general guidelines and how to set-up your development environment:

https://github.com/broadinstitute/hellbender/blob/master/README.md

R Required Packages

R packages can be installed using the install_R_packages.R script inside the scripts directory.

Create the jar file

./gradlew shadowJar

A jar file will appear in build/libs.

The CNV case and PoN workflows (description and examples)

This can be found here

Running the CNV case and PoN creation Workflows with premade Queue scripts

For Broad Internal instructions