Quantification of phase concordance. We illustrate the determination of local switch consistency using a hypothetical data
set from 10 heterozygous loci. The plotted circles represent the BAFs at each marker. The shaded haplotypes, h(g) and 
, represent the germline haplotypes, obtained by statistical estimation using the called genotypes. We call each allele in
haplotype h(b) by comparing each BAF to a threshold (depicted as a dotted line). Then we assess local switch consistency, indicated in vector
x, between the two haplotype reconstructions at each pair of consecutive heterozygous markers by looking for a match between
h(b) and either h(g) or 
.
