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

What is the correct step? VQSR and CNNScoreVariants?



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    Kshama Aswath

    Hi Damian,

    I am a pretty new user of GATK pipeline myself and am drowned in reading documentation after documentation and many times end up finding out "new steps" to use accidentally on GATK search or google search or through blogs etc.

    There is tremendous amount of information out there and we always have to choose what best fits our final goal.

    Having said that, I can share what  I have figured out.

    Hopefully sharing this helps us both :)

    For germline analysis, on a large cohort > 100 exomes, that I have, I did VQSR (assuming you did everything in order until this according to the GATK best practices) then "apply VQSR". You could use Calculate genotype posteriors  ( you must have genotype likelihood info from haplotype caller to do this) to sort of further assess and quantify uncertain genotype calls , then redo variant filtration and variant annotator  to get the ones that are not called by GATK/ or not in known spectrum aka novel ones out and then take it through Michigan imputation to validate it further.

    I found this paper super useful in understanding more, check this out:

    This GATk document also helps with further steps:

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    Bhanu Gandham

    Kshama Aswath


    Thank you so much for sharing your GATK experience here. Your interactions and suggestions will help build the knowledge base of this forum and help other scientists with their research :)

    The GATK team greatly appreciates your contribution!

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