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

unexpected variant calls by Mutect2 depending on ExtractIlluminaBarcodes --MAX_MISMATCHES

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    Pamela Bretscher

    Hi myourshaw,


    I am going to move your post into our Community Discussions -> General Discussion topic, as the somatic topic is for reporting bugs and issues with GATK.
    You can read more about our forum guidelines and the topics here: Forum Guidelines.


    Best,
    Pamela

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    Genevieve Brandt (she/her)

    Hi myourshaw,

    Could you give some specific examples of what you are seeing? More specific examples of a difference you see when MAX_MISMATCHES is 0 and 1 would help us problem solve to figure why the tools are behaving this way.

    Please also provide your complete commands.

    Best,

    Genevieve

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