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.


Return to top


See also General Documentation | Tool Docs Index Tool Docs Index | Support Forum

GATK version 4.0.0.0 built at 10-58-2018 11:58:10.