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We make no judgment as to the inheritance state of any region which does not fall within the above stated parameters.
Each assignment s is called an inheritance state.
Specifically, at a heterozygous locus, there is exactly one inheritance state that satisfies the children's haplotypes.
A descent graph describes the inheritance state of each allele and provides pedigrees guaranteed to be consistent with Mendelian sampling.
Haploscribe implements a parsimony approach to generate meiosis-indicator (inheritance state) vectors and uses a hidden Markov model (HMM) to deduce haplotypes spanning entire chromosomes.
A combination of pedigree data and statistical phasing based on inheritance state analysis was then used to infer phase for the majority of positions in each child's genome.
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At homozygous loci, all the inheritance states are allowed.
Finally, notice that the two heterozygous inheritance states (0, 1, 1, 0) and (1, 0, 0, 1) are arbitrarily labeled.
To define the inheritance states of neighboring SNVs in the family quartet, Dewey et al. first used a heuristic algorithm that binned allele assortments, followed by a HMM in which the hidden states corresponded to the four possible inheritance states in the quartet and the two error states described by Roach et al. [ 64].
Phasing information obtained through the sequencing of the genomes of family members maps recombinations and inheritance states at high resolution, highlighting the regions of the genome where causal variants segregate.
The transition probabilities are given by P ij = θ H (i, j )(1 - θ 4 -H (i, j ) where H i, j) is the Hamming distance between inheritance states i and j.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com