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

normal sample AF in Mutect2 paired mode


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    David Benjamin

    The AFs emitted by Mutect2 are the means of the posterior distribution on cell fraction conditioned on a variant existing.  The AF of 0.032 you see, for example, means "if this variant is really present in the normal (not that Mutect2 thinks it is), then our best guess of its allele fraction in the normal sample's cells is 0.032".

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