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

Difference between variants detected using gatk 4.1.8.1 and 4.1.9.0

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    Anthony Dias-Ciarla

    Hi Nefté Yañez,

    Thank you again for writing to the GATK forum! I appreciate you taking the time to repost in our support language. I hope that we can help you sort this out.

    When reviewing your inquiry, I noticed a couple of things. Firstly, both of the versions of GATK (4.1.8.1 & 4.1.9.0) that you used are out-of-date. Additionally, you mentioned that you ran Mutect2 with a Panel of Normals (PoN) composed of 30 samples. 

    1. We always recommend you use the latest release of GATK (4.2.6.1), as many bugs from previous versions are already corrected.
    2. We strongly recommend you use a PoN of at least 50 samples when running Mutect2.

    That said, I recommend you try upgrading to the latest version of GATK and running Mutect2 again with at least 50 samples in your PoN. If the discrepancy persists after implementing these changes, we will hopefully better understand both the origin of the problem and our best next steps.

    I’ve included the latest tool index for Mutect2 here and our technical documentation on creating PoNs here.

    I hope this helps! Please let us know if these suggestions lead you to success. If you require any further clarification or if other questions arise, please do not hesitate to reach out. 

    Best,

    Anthony

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    Anthony Dias-Ciarla

    Hi Nefté Yañez,

    We haven’t heard from you in a while so we will be closing out your ticket in our system. If you still require assistance, you need only respond to this thread, and we’ll make you a follow-up ticket to pick up where we left off.

    Thank you again for contributing to our GATK forum!

    Best,
    Anthony

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