Partek Genotype likelihood method utilizes observed base frequencies to calculate the genotype with the maximum likelihood at each genomic position based upon expected allele frequencies for heterozygotes and homozygotes and assuming a constant error probability. This method can identify single nucleotide variants but not insertions/deletions.

When a homozygous genotype would be observed, you would expect to observe nearly 100% of the homozygous allele. When the base frequencies of a heterozygous base are