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

Mixing up GATK versions



  • Official comment
    Genevieve Brandt (she/her)

    Hi wannamd,

    In order to run this step successfully without recreating your GVCFs you will need to use the --allow-old-rms-mapping-quality-annotation-data argument. You can still proceed just fine but the warning is letting you know that your MQ annotation results may not be reliable so you should use other annotations to reference the quality of your variant calls.



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    Anton Kovalsky

    Hi wannamd

    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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