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

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    Robert Bremel

    Perhaps the problem is because  -normal  argument (about #75 in -help) is actually a required input in order to keep one's samples sorted out properly

     It is not specified as a "Required Argument"  by Mutect2 -help

    In reality it isn't and "Optional Argument"  :-)

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    Genevieve Brandt (she/her)

    Hi Robert, thanks for the update. It seems that the --normal argument is required for your use case. For more use cases, here is the tool documentation

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