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

disabling NotDuplicateReadFilter in Mutect2



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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.

    For context, check out our support policy.


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    Hi jungmin choi,

    There are arguments that you can apply with Mutect2 (and other GATK tools) to either disable specific read filters (--disable-read-filter) or all default read filters (--disable-tool-default-read-filters). Further information can be found on the Mutect2 documentation page.

    I hope this is helpful.

    Kind regards.

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