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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

Mutect2: NuMTs filtering on RNA-seq



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    Bhanu Gandham

    Hi ,

    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.

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    Genevieve Brandt (she/her)

    Hi Leore Nehemie Bensabath,

    This should work, provided that you interpret autosomal coverage correctly. The autosomal coverage represents the average coverage of the autosome in the BAM. For RNA, it would represent how much autosomal RNA is in your BAM. So, the value might be different with RNA seq but it won't change your ability to use the flag.



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