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

Running Mutect 2 with matched normal vs tumor mode

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    Mommy Misato

    If you could also confirm for me the default read depth that Mutect2 does. I've read somewhere that its 50 but I would like confirmation. Thanks!

     

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    Pamela Bretscher

    Hi Mommy Misato,

    The result you are seeing is expected because when you do not have a matched normal sample, Mutect2 will call all germline variants in addition to somatic variants. You can find more information about the differences between tumor-only and matched-normal mode in the Mutect2 FAQ. As for your second question, I am not sure what value you are referring to as Mutect2 accommodates a wide range of read depths. You can find information about the default values for various parameters in Mutect2 in the tool documentation. I am going to move your post to the General Discussion topic as the Somatic topic is for reporting bugs with GATK.

    Kind regards,

    Pamela

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    Mommy Misato

    Thank you!

     

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