This repository contains the next generation of the Genome Analysis Toolkit (GATK). The contents of this repository are 100% open source and released under the BSD 3-Clause license (see LICENSE.TXT).

GATK4-Power

Supporting GATK4 on IBM Power architecture, including enablement, performance tuning and optimization. The package is built from source code with adding PairHMM native library for supporting Power VSX/Altivec extension.

• Latest version v4.1.8.0 built on 07-02-2020
• Older version See other branches

This includes:

• GATK4 package built on IBM Pwer9 GATK4 on Power9 full package (downloadable) is available upon request.
• Benchmarking scripts to run GATK4 pipelines on IBM Power system

Install GATK4 on Power9

• Clone GATK4-Power git clone
• Run installation script to complete the installation ./install_gatk4-power9
• Generate runscript (Germline) ./run_gatk-power

Create docker image

• Run docker script and upload to your system docker run -t gatk:4.1.8.0

Performance

Contact: Ruzhu Chen (ruzhuchen@us.ibm.com) for support

• Note to user: The Power9 download is password protected. Please contact me for more info.