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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    Monete Rajão Gomes

    Hi all, *Hope everyone is okay*

    I need some help here, with VQSR command recomendations.

    I've read this documentation and soon we will try to run VQSR steps (on latest GATK version).

    I'm using GATK since v3.8. Previously, there are some advices about command line for VQSR, ti/tv threshold, database resources, etc, both for genome and for exome data.

    Also, I was wondering where is this tutorial on this new website.
    Further, I think the FAQ link that can possibly explain about this (referenced here in "CAVEAT" section, image below), is not working.

    FAQ link not working


    Are there any recommendations different from GATK v3.8, or should I use the same?

    SNP mode

    Indel mode

    Also, some annotations used on GATK 4 have their names changed (comparing with GATK v3.8), haven't they?

    Thank you for you time and patience.


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    Jordi Pérez-Tur

    Hi there,

    Just for the info. All the links in this paragraph:

    VQSR is probably the hardest part of the Best Practices to get right, so be sure to read the method documentationparameter recommendations and tutorial to really understand what these tools do and how to use them for best results on your own data.

    are also dead (at least as of Sept 2020).



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    Jacob Shujui Hsu

    I can confime that the links for VQSR are still missed (May 2021). 

    Also, I found a VQSR parameter discrepancy for omni dataset usage.

    Above post indicate the setting from 3.8 and here 


    Here is the parameter I found in this post :



    Q1: Why are they different? I can not find any post discussing this issue. 

    Q2: Because of the discrepancy above, the parameter recommendations would be needed more than ever. I can not even find the para recommendation for INDEL. 


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