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