Gatk4

Introduction

GATK (Genome Analysis Toolkit) is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discovery.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/gatk4

Home page: https://www.broadinstitute.org/gatk/

Versions

• 4.2.6.1

• 4.3.0.0

Commands

• gatk

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run gatk4 on our clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=gatk4
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load gatk4/XXXX ### you can run *module avail gatk4* to check all available versions

gatk --java-options "-Xmx12G -XX:ParallelGCThreads=24" HaplotypeCaller \
     -R hg38.fa -I 19P0126636WES.sorted.bam \
     -O 19P0126636WES.HC.vcf --sample-name 19P0126636