Say, allele A and B define haplotype 1. allele A, B and C define haplotype 2.
If we identify A, B and C at the same time, two situation may occur: 1) they all could exist in the same chromosome. 2) A and B in one chromosome and C in another chromosome.
This opens ambiguity between genotype 1* and 2. We can't just assume A, B and C are most likely in the same chromosome (statistically linked) because that way genotype 1 won't exist, right?
Any comments are appreciated!