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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

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Tutorials

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  • (How to) Map and clean up short read sequence data efficiently
    (How to) Map and clean up short read sequence data efficiently In this tut...
  • (How to) Map reads to a reference with alternate contigs like GRCH38
    This document was written for GATK3. Some commands or information may be out ...
  • (How to) Fix a badly formatted BAM
    This document was written for GATK3. Some commands or information may be out ...
  • (Notebook) Concordance of NA19017 chr20 gCNV calls
    This notebook shows how to perform the analysis that is alluded to in this tu...
  • (How to part II) Sensitively detect copy ratio alterations and allelic segments
    Document is currently under review and in BETA. It is incomplete and may cont...
  • (How to) Run GATK in a Docker container
    This document explains how to install and use Docker to run GATK on a local m...
  • (How to) Consolidate GVCFs for joint calling with GenotypeGVCFs
    In GATK4, the GenotypeGVCFs tool can only take a single input i.e., 1) a sing...
  • (How to) Create a Spark cluster on Google Dataproc
    As noted in our brief primer on Dataproc, there are two ways to create and co...
  • (How to) Call common and rare germline copy number variants
    The tutorial outlines steps in detecting germline copy number variants (gCN...
  • (How to) Call somatic mutations using GATK4 Mutect2
    This tutorial is applicable to Mutect2 version 4.1.1.0 and higher. Post sugge...
  • Funcotator Information and Tutorial
    This page explains what Funcotator is and how to run it. Table of Contents...
  • (How to) Run the Pathseq pipeline
    Beta tutorial Please report any issues in the comments section. Overview Pa...
  • (Notebook) Correlate gCNV callset metrics and annotations
    This notebook examines gCNV callset annotations using data from this tutorial...
  • (How to) Run Spark-enabled GATK tools on a local multi-core machine
    This is a placeholder for a document in progress.
  • (How to) Install and use Conda for GATK4
    Some tools in GATK4, like the gCNV pipeline and the new deep learning variant...
  • (How to) Filter variants either with VQSR or by hard-filtering
    This document is in BETA. It may be incomplete and/or inaccurate. Post sugges...
  • (How to) Run Spark-enabled GATK tools on a Spark cluster
    This is a placeholder for documentation in progress.
  • (How to part I) Sensitively detect copy ratio alterations and allelic segments
    Document is currently under review and in BETA. It is incomplete and may cont...
  • (How to) Filter on genotype using VariantFiltration
    Before using VariantFiltration, please read the entirety of the discussion in...
  • (How to) Call somatic mutations using GATK4 Mutect2 (Deprecated)
    This tutorial is now deprecated and only valid for Mutect2 v4.1.0.0 and lower...
  • (How to) Execute Workflows from the gatk-workflows Git Organization
    The gatk-workflows git organization houses a set of repositories containing w...

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