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.
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written
by
g.zachwyc •
1 answer
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
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