Usage

We provide a wrapper script GenomeAnalysisTK for gatk module versions before 4.0 that is equivalent to running:

mkdir -p tmp
export TMPDIR=$(pwd)/tmp
java -Djava.io.tmpdir=$TMPDIR -cp /apps/gatk/jexl/2.1.1/commons-jexl-2.1.1.jar -jar $HPC_GATK_DIR/GenomeAnalysisTK.jar

If you do not use the wrapper you must make sure to create and use a local TMPDIR in your /blue space with GenomeAnalysisTK.jar. Otherwise /tmp will be used by default leading to filled up /tmp partitions on compute nodes and node failure.

Starting with GATK4 new upstream wrappers are available, so we no longer include our own wrapper. GenomeAnalysisTK and gatk. Running GenomeAnalysisTK will show you how to run gatk tools. To get a full list of tools run gatk list.