What is GATK
GATK, properly pronounced “Gee-ay-tee-kay” (/dʒi•eɪ•ti•keɪ/) , stands for Genome Analysis Toolkit. It is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discovery. The tools can be used individually or chained together into complete workflows.
To setup required environment variables, please use following command
|HPC2015||module load gatk|
|HPC2021||module load gatk|
Sample SLURM batch script for GATK4 using Singularity image is located under /share1/gatk/sample/ in HPC2021 system.