ChromosomeCounts

Counts and frequency of alleles in called genotypes (AC, AF, AN)

Category Variant Annotations

Overview

Counts and frequency of alleles in called genotypes

This annotation outputs the following:

Number of times each ALT allele is represented, in the same order as listed (AC)
Frequency of each ALT allele, in the same order as listed (AF)
Total number of alleles in called genotypes (AN)

Example

AC=1;AF=0.500;AN=2

This set of annotations, relating to a heterozygous call(0/1) means there is 1 alternate allele in the genotype. The corresponding allele frequency is 0.5 because there is 1 alternate allele and 1 reference allele in the genotype. The total number of alleles in the genotype should be equivalent to the ploidy of the sample.

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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.