What is GATK?

GATK (Genome Analysis Toolkit) is a software package developed by the Broad Institute for variant discovery and genotype refinement in high-throughput sequencing data. It's widely used in genomic research and clinical settings to identify single nucleotide polymorphisms (SNPs), insertions/deletions (indels), and structural variants from next-generation sequencing (NGS) data. The toolkit provides a comprehensive suite of tools for data preprocessing, variant calling, and variant filtering, following best practices for accuracy and reproducibility.