SLRP does not produce whole chromosome haplotypes. It only phases regions of the genome where IBD sharing is detected, and can only resolve the phase of heterozygous sites when at least one of the individuals sharing IBD is homozygous at those loci. This complicates the calculation of SE between methods. We treated each of the IBD segments inferred by SLRP separately and evaluated SE within these regions. We refer to this metric as the “within IBD SE”, using it to evaluate SLRP's performance against methods that phase every site. We also calculated the SE of the SHAPEIT2, Beagle and HAPI-UR haplotypes across the whole of chromosome 10. We also report the yield of SLRP, defined as percentage of genotypes that are phased.
