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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

GATK Muteck2 missing call



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    Anthony DiCi

    Hi Marco Chiapello,

    Thank you for writing to the GATK forum! I hope that we can help you sort this out.

    I brought the issue you encountered to our developers and received some feedback.

    The team first noticed that you are running Mutect2 in gvcf-mode, which they created for rare instances of variant-calling in mitochondria. Even then, our users mostly use gvcf-mode for edge cases. Secondly, you are running the tool without a Panel of Normals (PoN). We strongly recommend running Mutect2 with a PoN containing at least 50 samples.

    That said, there are a couple of action items before we can move forward with diagnosing your problem. 

    1. Please confirm that the command line you included is the entire command you used when running the tool.
    2. Please try re-running Mutect2 again in regular vcf-mode.

    If you are still having trouble after re-running, please respond with your full command line, and I will bring it back to our developers to figure out our next steps.



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    Anthony DiCi

    Hi Marco Chiapello,

    We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!

    Kind regards,


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