3.10.2. Frequency Aware Zygosity

This algorithm computes the zygosity of a sample by using the individual’s genotype combined with frequency information available in a variant frequency catalog such as ExAC or 1000 genomes. The zygosity is categorized as follows:

  • Homozygous Major: Two major alleles called (Wild Type)

  • Homozygous Minor: Two minor alleles called

  • Heterozygous: Two different alleles called

  • Hemizygous Major: A single major allele called on sex chromosome (Wild Type)

  • Hemizygous Minor: A single minor allele called on sex chromosome

The advantage to using frequency information when computing zygosity is that the reference sequence contains an alternate allele at certain positions. The alternate allele frequency at this position is often greater than 90%. We denote the most common allele as the major allele.


At a site with multiple alternate alleles, the major allele could have a frequency less than 50% (eg. Ref = 35%, Alt1 = 20%, Alt2 = 45%)


Requires a genotype (GT) sample level field.

This algorithm requires first annotating variants using a variant source with an Alternate Allele Frequency field.


Creates a categorical field denoting the frequency aware zygosity for each sample.