Overview

The Genome Analysis Toolkit (GATK) is a software package for analysis of high-throughput sequencing data, developed by the Data Science Platform group at the Broad Institute. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as data quality assurance.

Best Practices

GATK is famous for its "Best Practices" workflows—step-by-step recommendations for performing variant discovery in germline and somatic contexts, as well as RNA-seq variant calling.

Core Tools

• HaplotypeCaller: The standard tool for calling germline SNPs and indels via local de-novo assembly of haplotypes.
• Mutect2: Designed for somatic mutation calling (tumor vs normal).
• VQSR: Variant Quality Score Recalibration for filtering raw variant calls.