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Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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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. Learn more

  1. GATK
  2. Getting Started
  3. Best Practices Workflows

Best Practices Workflows

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  • Getting started with GATK4
    GATK (pronounced "Gee-ay-tee-kay", not "Gat-kay"), stands for GenomeAnalysisT...
  • Germline copy number variant discovery (CNVs)
    Purpose Identify germline copy number variants. Diagram is not available ...
  • Pipeline Index
    This document is under construction. It aims to provide an overview of use ca...
  • Somatic short variant discovery (SNVs + Indels)
    Purpose Identify somatic short variants (SNVs and Indels) in one or more tum...
  • Germline short variant discovery (SNPs + Indels)
    Purpose Identify germline short variants (SNPs and Indels) in one or more in...
  • Data pre-processing for variant discovery
    Purpose The is the obligatory first phase that must precede all variant disc...
  • Somatic copy number variant discovery (CNVs)
    Purpose Identify somatic copy number variant (CNVs) in a case sample. Requir...
  • About the GATK Best Practices
    This document provides important context information about how the GATK Best ...
  • RNAseq short variant discovery (SNPs + Indels)
    Purpose Identify short variants (SNPs and Indels) in RNAseq data. Ref...

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