gatk
Link to section 'Introduction' of '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/.
Link to section 'Versions' of 'gatk' Versions
- 3.8
Link to section 'Commands' of 'gatk' Commands
- gatk3
Link to section 'Module' of 'gatk' Module
You can load the modules by:
module load biocontainers
module load gatk
Link to section 'Example job' of 'gatk' 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 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