Showing tool doc from version 4.1.3.0 | The latest version is 4.1.3.0

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 Documentation Index | Support Forum

GATK version 4.1.3.0 built at Fri, 9 Aug 2019 21:16:03 -0400.