THIS CODEBASE HAS BEEN DEPRECATED - WE ARE NO LONGER MAINTAINING IT.

PLEASE SEE https://github.com/broadinstitute/gatk INSTEAD

DEPRECATION NOTICE


GATK4-Protected (codename Hellbender-protected)

GATK4 development of the previously license-protected part of the toolkit. The contents of this repo will be merged into broadinstitute/gatk in the near future.

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

Read GATK 4 README

Please refer to the GATK 4 public repo README for general guidelines and how to setup your development environment.

Requirements

R Required Packages

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

Building GATK4

Running GATK4

Testing GATK4

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