Haplotyping and Verification by Long-Fragment Sequencing
We inferred recombination positions and haplotypes of the family by using our software tool Ped-IBD.33 Haplotype blocks are defined by recombination positions. We identified a total of 813 recombination positions over 22 chromosomes. Haplotype blocks range in size from 0.02 to 12 Mb (90% interval) and have a median length of 1.65 Mb. We further confirmed haplotyping results with molecular haplotypes from the LFR technology in three individuals (NA12877, NA12885, and NA12886; Table S3). The comparison showed that phasing was 99.84% to 99.92% concordant between inferred and molecular haplotypes.