GATK
GATK (Genome Analysis ToolKit) is a collection of tools maintained by the Broad Institute for analysing NGS data.
How to use on KewHPC
To use GATK first load the module
module load gatk/4.2.0.0
Then activate the conda environment. If you've not used conda before initialise it as described here
conda activate gatk
do deactivate the conda environment:
conda deactivate
Now you can see the available tools:
gatk --list