Software: GATK
Description
GATK (Genome Analysis Toolkit) is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discovery.
Available Versions
| Unspecified: | 3.8 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/gatk and its home page: https://www.broadinstitute.org/gatk/.
Commands
- gatk3
Module
You can load the modules by:
module load biocontainers
module load gatk
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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