GATK

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 its website: https://biocontainers.pro/tools/gatk and its home page: https://www.broadinstitute.org/gatk/.

Versions

• 3.8

Commands

• gatk3

Module

You can load the modules by:

module load biocontainers
module load 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 GATK on our clusters:

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

module --force purge
ml biocontainers gatk

gatk3 -T HaplotypeCaller  \
    -nct 24  -R hg38.fa \
    -I 19P0126636WES.sorted.bam \
     -o 19P0126636WES.HC.vcf