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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 filter : clustered_events definition

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    David Benjamin

    "Clustered" mean co-occurring in the same local assembly interval, usually about 200bp.  By the way, you should upgrade to the most recent release of GATK 4.  The GATK 3 version of Mutect2 is obsolete.

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    whynot

    Thanks for answer!

     

    Can I have one more question?

     

    I got new information about clustered_events filter.

    When they count 'clustered' variants, they have another condition:

    "variants with distance between >= 3 bp"

    The reason I thought this condition was true is that if the distance between variants in my vcf file is less than 3 bp, I did not get caught by the clustered_events filter.

    Is that really right condition?

    If that's right, then "clustered" mean co-occurring in the same local assembly interval, about 3-200bp?

     

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    David Benjamin

    I think the intent was to avoid filtering MNPs.  We do it differently in GATK 4.  I can't emphasize enough how important it is to upgrade to the most recent GATK 4 version.

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    Dario

    Is there a table of filters containing detailed definitions of all of the possible ones in a document somewhere? The VCF header ones are too short for readers who weren't involved with the development of the software.

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    David Benjamin

    The most current Mutect2 documentation can be found in our github repo here: https://github.com/broadinstitute/gatk/blob/master/docs/mutect/mutect.pdf

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