VCF AF and %Freq
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Entering edit mode
8 months ago
g.zachwyc • 0

Hello! Allele frequency (AF) for a variant at a particular position in my unannotated VCF file doesn't match the %Freq of the alternative base of the variant in the annotated file. Could someone please explain why that could be? Many thanks.

VCF allele frequency Allele frequency frequency • 474 views
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Entering edit mode
8 months ago
steve ★ 3.0k

Some variant callers apply extra statistical modeling corrections to the reported allele frequencies. There can also be extra filters applied before/after the reported metrics are calculated.

examples; https://gatkforums.broadinstitute.org/gatk/discussion/23408/mutect2-ad-does-not-match-af

https://gatkforums.broadinstitute.org/gatk/discussion/comment/56103

https://gatk.broadinstitute.org/hc/en-us/community/posts/360057830232-Wrong-Calculation-of-DP-AD-AF

https://github.com/broadinstitute/gatk/issues/6067

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