GATK¶
GATK is a collection of command-line tools for analysing high-throughput sequencing data with a primary focus on variant discovery.
GATK is available as a module on Apocrita.
Usage¶
To run the default installed version of GATK, simply load the
gatk module:
$ module load gatk
$ gatk -h
Usage: gatk <subcommand> [arguments]
For full usage documentation, run gatk -h.
Example job¶
Serial job¶
Here is an example job running on 1 core and 2GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G
module load gatk
# Run HaplotypeCaller in default mode on a single input BAM file containing
# sequence data and outputs a VCF file containing variant calls.
gatk HaplotypeCaller -R reference.fasta -I sample1.bam -O variants.vcf