We estimated haplotypes from GLPhase genotype calls using SHAPEIT312. Chromosomes were phased in chunks consisting of 16,000 variants plus 3,300 variants overlapping with neighboring chunks on either side. The non-default command line option -w 0.5 was used for SHAPEIT3. Chunks were ligated using the ligateHAPLOTYPES program (see URLs). SHAPEIT3 does not handle multiple variants at the same genomic coordinate, so multiallelic sites (SNPs with 3 or 4 alleles) were shifted by one or two base pairs for rephasing, and then moved back to their original position after chunk ligation.
