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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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.

License

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

Available

  • Roihu: 4.5.0.0, 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/4.5.0.0

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/4.5.0.0

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

More information