To estimate the heritability for a particular genomic segment we compute the genetic relatedness matrix as defined in Yang et al10, replacing genotypic for local ancestry calls, and restricting to just those SNPs contained in the region of interest. Given a partitioning of segments along the genome (in our case 22 segments), it is possible to fit them individually or jointly. We attempted both approaches, but found that the joint fit produced a numerical instability in the optimization algorithm preventing convergence. Thus all results reported for the single chromosome analyses are provided by individual and not joint estimates.
