Fig. 9

Nested genotyping procedure. Nodes with numbers mark the start and end of variant sites. In each panel, blue-filled nodes mark which site is being processed, red-filled nodes mark called alleles, and red paths mark alleles considered for genotyping. Ref is the reference allele, Alts are the alleles considered for genotyping, and GT is the called genotype. The example shows haploid genotyping. a Genotyping of child site 2. Allele “G” gets called. b Genotyping of child site 3. Allele “CC” gets called. c Genotyping of parent site 1. Alts are generated from the alleles called in child sites 2 and 3: allele “G” is used from site 2, and allele “CC” is used from site 3, producing alleles “AGT” and “CC”. Allele “AGT” gets called, going through site 2. d In c, the path going through site 2 was called. Because genotyping is haploid, the call at site 3 is invalidated (GT becomes “null”)