Rapid haplotype inference for nuclear families

Table 5 States at a fully informative for one parent locus built from a state with ambiguous values

		p ₀	p ₁	c ₀	c ₁	c ₂	c ₃	c ₄	# Rec
Prev	$\vec{v}$			〈0, 1〉	〈1, 1〉?	〈1, 1〉	〈0, 0〉?	〈1, 1〉	0
State	hap	〈a, g〉	〈a, a〉	〈g, a〉	〈a, a〉	〈a, a〉	〈a, a〉	〈a, a〉	4
a	$\vec{v}$			〈1, 1〉	〈0, 0〉	〈0, 1〉	〈0, 0〉	〈0, 1〉
State	hap	〈g, a〉	〈a, a〉	〈g, a〉	〈a, a〉	〈a, a〉	〈a, a〉	〈a, a〉	1
b	$\vec{v}$			〈0, 1〉	〈1, 1〉	〈1, 1〉	〈1, 1〉	〈1, 1〉

An example, modified from Table 3 and not from real data, showing a state with ambiguous inheritance values (marked by ?) at the previous locus, and the two states Hapi builds based on it. For unambiguous children's inheritance vector values, the system copies the bits corresponding to the homozygous parent from the previous state. For ambiguous children, two opposite inheritance values are valid for the previous state, and the system uses the homozygous parent bit from the inheritance value that matches the heterozygous parent's bit in the state being built. Both of the two inheritance values are necessarily represented, one in each of the resulting states. As the underlined values show, the inheritance values for the homozygous parent differ across the two outputs. As such, the states are not equivalent, and Hapi cannot eliminate either. Bold values indicate recombinations.

ISSN: 1474-760X