its default MCMC options (-Ne 20000 -k 80) for autosomes and -Ne 15000 -k 100 for X chromosome. SHAPEIT was run without MCMC iteration (-no-mcmc) so that each sample was phased independently using the reference panel as the haplotype scaffold regardless of the phasing of the other samples. Single-sample VCFs were merged together and INFO scores were re-calculated from genotype posterior probabilities (GPs). Variants with INFO score less than 0.4 were excluded from further analysis. Cell lines originating from the same donor were checked for possible sample swaps using BCFtools (bcftools gtcheck -G1). Swapped samples typically had large number of discordant genotypes (>20%), whereas in samples from the same donor the number of discordant genotypes was low (<0.3%), even in the presence of large copy number variation.
