Fifteen Years of the Genome Analysis Toolkit as the De Facto Standard in Short-Read Variant Calling

Abstract

Genome Analysis Toolkit (GATK) is a rigorously maintained collection of 430 analysis tools and a core bioinformatics engine. First released in 2010 as a toolkit for next-generation sequencing (NGS) data analysis, GATK remains one of the least celebrated yet foundational tools of the NGS era. By employing state-of-the-art approaches and continuously adapting to the evolving demands of NGS analysis, it has effectively unified the variant calling process worldwide. In a field as rapidly evolving as genomics, it is remarkable that, over a decade later, the same toolkit remains the gold standard. This critical review explores the pre-history of GATK, the reasons for its broad and enduring adoption by the scientific community, its developmental evolution, contributions to science, and future prospects. Keywords: genome analysis toolkit, GATK, variant calling, DNA, NGS