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GATK

GATK is a collection of command-line tools for analyzing 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 2G 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

References