Participant genotype data were imputed against the September 2013 release of 1000 Genomes Phase1 reference haplotypes, phased with ShapeIt229. We phased using an internally developed phasing tool, Finch, which implements the Beagle haplotype graph-based phasing algorithm30, modified to separate the haplotype graph construction and phasing steps. Finch extends the Beagle model to accommodate genotyping error and recombination, to handle cases where there are no consistent paths through the haplotype graph for the individual being phased. We constructed haplotype graphs for European samples on each 23andMe genotyping platform from a representative sample of genotyped individuals, and then performed out-of-sample phasing of all genotyped individuals against the appropriate graph.
