For each SNP, the emission probability for a state of 2 copies is the union of the three normal distributions specified by Birdseed (modeling the AA, AB and BB clusters). The natural copy number variation inherent to the individual alleles across these clusters allows for direct estimation of the null, A, B, AAB, ABB and AABB clusters. (Future iterations could model and compensate for crosstalk between the two alleles9.) Emission probabilities for increasing dosages of each allele are imputed similar to copy number probes.
