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

MuTect2: There are too many keys for the sample

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    nilshomer

    --VALIDATION_STRINGENCY SILENT and --CREATE_INDEX false have no effect.

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    nilshomer

    Closing, looks like the file got overwritten and MuTect2 is giving a proper error.

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    Genevieve Brandt

    nilshomer thanks for posting your solution!

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