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Genome Analysis Toolkit (GATK)

Definition
AI-generated

The Genome Analysis Toolkit (GATK) is an open-source software suite, developed at the Broad Institute, for analyzing high-throughput sequencing data.

Topics
Sequencing Data Analysis Bioinformatics
URL
https://gatk.broadinstitute.org/
Related
Base Quality Score Recalibration (BQSR) Duplicate marking Genomic Variant Call Format (gVCF)

Why it matters in GWAS

Many large sequencing studies that supply variants for association analysis, imputation panels, or rare-variant tests document GATK-based calling and QC; knowing the toolkit helps interpret methods sections, filter fields, and reproducibility choices.

Example usage

"Variants were called with GATK best practices, including BQSR and joint genotyping across all samples."

Base Quality Score Recalibration (BQSR) Duplicate marking Genomic Variant Call Format (gVCF) GenomicsDB HaplotypeCaller Joint genotyping Parabricks Picard Variant Calling
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • McKenna A, et al. (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research. https://doi.org/10.1101/gr.107524.110
  • DePristo MA, et al. (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics. https://doi.org/10.1038/ng.806
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