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

Best practice to process a multisample mutect2 vcf



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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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    David Benjamin

    Jenifer This is a totally reasonable thing to want to do, but it's not within the scope of our pipeline.  The Mutect2 (along with FilterMutectCalls, of course) pipeline generates variant calls from one or more tumor and normal samples from a single individual.  We don't have any tools for comparing variant calls from different individuals, except for a few simple operations in SelectVariants.

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