GATK

GATK (Genome Analysis Toolkit) is a collection of tools for variant discovery and genotyping in high-throughput sequencing data, developed at the Broad Institute.

GATK

License

GATK4 is open source and free to use. See the GATK licensing information.

Available

Roihu-CPU: 4.5.0.0, 4.7.0.0, via the bio-apps module.

Usage

GATK is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the GATK module:

module load bio-apps/v202603
module load gatk/4.7.0.0

GATK tools are run through the gatk wrapper, followed by the tool name. Java options such as the heap size can be passed with --java-options:

gatk --java-options "-Xmx8g" HaplotypeCaller -R reference.fa -I input.bam -O output.vcf.gz

Example batch script

#!/bin/bash
#SBATCH --job-name=gatk
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=12:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=10G

module load bio-apps/v202603
module load gatk/4.7.0.0

gatk --java-options "-Xmx8g" HaplotypeCaller -R reference.fa -I input.bam -O output.vcf.gz

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk