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AlleleFraction

Variant allele fraction for a genotype

Category Variant Annotations


Overview

Variant allele fraction for each sample.

This annotation describes the proportion of the sample's reads that support the variant allele(s). It uses only reads that are actually considered informative by HaplotypeCaller (HC) or Mutect2, using pre-read likelihoods that are produced internally by HC/Mutect2.

In this context, an informative read is defined as one that allows the allele it carries to be easily distinguished. In contrast, a read might be considered uninformative if, for example, it only partially overlaps a short tandem repeat and it is not clear whether the read contains the reference allele or an extra repeat.

See the method documentation on using coverage information for important interpretation details.

Caveats

  • If a genotype is already annotated with allele fraction (as by the SomaticGenotypingEngine if `--get-af-from-ad` is not specified), the value will not be recalculated.

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GATK version 4.1.0.0 built at Wed, 30 Jan 2019 10:21:04 +0530.