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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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FAQ

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  • Which training sets arguments should I use for running VQSR?
    This document describes the resource datasets and arguments that we recommend...
  • FAQ for Mutect2
    Here is a collection of questions related to Mutect2 that we frequently find ...
  • What is physical phasing?
    In the format field of a PGT (Pre-Implantation Genetic Testing) VCF, you may ...
  • Where can I get the GATK source code? Is it open-source?
    YES! Starting with GATK4 it is fully open-source under a BSD 3-clause license...
  • Are there Best Practices for calling variants in RNAseq data?
    We are working on updating our recommended workflow for calling variants in R...
  • Does GATK work on non-diploid organisms?
    YES! In general most GATK tools don't care about ploidy. The major exception...
  • How should I cite GATK in my own publications?
    To date, we have published three papers on GATK, a preprint in bioRxiv (citat...
  • Where can I find known variants, training and truth sets, and other resource files?
    For general definitions of these terms, see this Dictionary entry. Humans I...
  • How can I make GATK tools run faster?
    It sure seems like everyone has a need for speed these days. So, there are tw...
  • How can I attend or host a GATK workshop?
    The list of upcoming workshops is available in the Events calendar. The cou...
  • When should I restrict my analysis to specific intervals?
    This document covers the reasoning behind the use of genomic intervals. If yo...
  • What are the requirements for running GATK?
    Contents Skills Input data Software Hardware 1. Skills / experience W...
  • How should I prepare for a GATK workshop?
    So you're going to a GATK workshop? Fantastic! We're looking forward to guidi...
  • Can I get a notification when my question is answered or commented on?
    Yes, absolutely! By default, the site will send notifications about replies ...
  • Can I use different versions of the GATK at different steps of my analysis?
    Short answer: NO, unless it's a combo that we made. Medium answer: No, at le...
  • How should I pre-process data from multiplexed sequencing and multi-library designs?
    Our Best Practices pre-processing documentation assumes a simple experimental...
  • What input files does the GATK accept or require?
    Analyses done with the GATK typically involve several (though not necessarily...
  • What types of variants can GATK tools detect or handle?
    The answer depends on what tool we're talking about, and whether we're consid...

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