gatk-software
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Table of Contents
Genome Analysis ToolKit (GATK)
GATK offers a wide variety of tools with a primary focus on variant discovery and genotyping.
Information
- Latest Version: 4.2.2.0
- Added: May, 2014
- Updated: September, 2021
Usage
See which versions of GATK are available:
$ module avail gatk
Load one version into your environment and run it:
$ module load gatk/4.2.2.0 $ gatk
Note: The HaplotypeCaller step can scale to multiple CPUs/threads. Please use the -nct
option to set the number of threads launched by GATK. This number should be the same number of CPUs requested in your SLURM batch job.
Installation
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://github.com/broadinstitute/gatk/releases/download/4.2.2.0/gatk-4.2.2.0.zip $ unzip gatk-4.2.2.0.zip $ sudo cp -r gatk-4.2.2.0 /export/apps/gatk/4.2.2.0
gatk-software.1631799522.txt.gz · Last modified: 2021/09/16 13:38 by aorth