allele at all SNPs identified in the phase 1 release of the 1000 Genomes Project. Reads that did not overlap any polymorphic sites were discarded. In the second step, the genotype likelihoods for all loci in all samples (with or without the reference panel of haplotypes, 381 in total for simulations) were passed to the Beagle imputation software12 with default parameters (i.e. “like” for the genotype likelihoods and “phased” for the reference haplotypes).
