Figure 1
Validation of SHaploseek by sequencing single cells from members of two families. We inferred the haplotypes of grown-up children based on ultra-low-pass genome sequencing of single lymphoblast cells from the children and low-pass sequencing of the parents and a reference child. The “unsampled” sequencing depths of the parent and reference child are given in Table 1. Other sequencing depths were obtained by down-sampling. Haploseek data is also presented for reference. The accuracy of inference of both maternal and paternal transmitted haplotypes is reported for each child (legend). (a) For Family 1, we plot the proportion of the 200,484 genome-wide array SNVs with high-confidence haplotype prediction (marginal probability > 0.99 or < 0.01) in non-ROC (regions of consanguinity) sites (y-axis). Results are shown for various values of the sequencing depth of the parents and the reference child, as well as for Haploseek (x-axis). (b) The phasing accuracy (based on ‘ground-truth’ haplotypes inferred from bulk DNA) at non-ROC SNVs with high-confidence prediction. (c, d) Same as (a) and (b), for Family 2.
