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.
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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