We divided each autosomal chromosome and the X chromosome into overlapping chunks (with chunk size of 1 Mb each and with 0.1 Mb overlap between consecutive chunks), and then phased each of the chunks using Eagle v.2.481. We removed all singleton sites and compressed the haplotype chunks into m3vcf format109. Afterwards, we ligated the compressed haplotype chunks for each chromosome to generate the final reference panel.
