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

selecting allele depth Mutect2

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    Genevieve Brandt (she/her)

    Hi Sonia Wolf,

    I would recommend using VariantFiltration to filter the variants by those two cutoffs then you can use SelectVariants to filter the file.

    If there is still an issue please also share the stack trace so we can confirm that there isn't something else going on.

    Best,

    Genevieve

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