gatk4
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/.
Link to section 'Versions' of 'gatk4' Versions
- 4.2.0
- 4.2.5.0
- 4.2.6.1
- 4.3.0.0
Link to section 'Commands' of 'gatk4' Commands
gatk
Link to section 'Module' of 'gatk4' Module
You can load the modules by:
module load biocontainers
module load gatk4/4.2.5.0
Link to section 'Example job' of 'gatk4' Example job
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