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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

performance of indel calling by MuTect2

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    Genevieve Brandt (she/her)

    Hi huan wang,

    The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

    Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

    We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

    For context, check out our support policy.

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    D B

    I'm also observing a rather abnormally high number of indels with Mutect2, specifically insertions. When comparing to a group of previously generated VCF files using the same data a couple years ago, I don't see as many indels present. I didn't examine it closer, but I assumed that it was due to the different GATK versions and flags utilized in the workflow.

    GATK version - v4.1.4.1

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    Genevieve Brandt (she/her)

    D B huan wang 

    We recently have made updates to Mutect2 so I would recommend first, use the most recent version. There is also a lot of information about Mutect2 on this forum, so please see other posts for more information. Here are documents about Mutect2 and how to troubleshoot the output (Some of the documents are why variants are not called, but they still have helpful info):

    If you cannot find an explanation after doing more examination, please make a thorough post with examples so that we can look into it.

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