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. Detailed usage can be found here: https://www.broadinstitute.org/gatk/.

Versions

• 4.2.0

• 4.2.5.0

• 4.2.6.1

• 4.3.0.0

Commands

gatk

Module

You can load the modules by:

module load biocontainers
module load gatk4/4.2.5.0

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 our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=gatk4
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers gatk4/4.2.5.0

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