GATK, pronounced "Gee Ay Tee Kay" (not "Gat-Kay"), stands for
GenomeAnalysisToolkit. 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.
end-to-end workflows are provided, called GATK Best Practices, tailored for
specific use cases.

Developed in the Data Sciences Platform at the Broad Institute, the toolkit
offers a wide variety of tools with a primary focus on variant discovery and
genotyping. Its powerful processing engine and high-performance computing
features make it capable of taking on projects of any size.

WWW: https://gatk.broadinstitute.org/hc/en-us