Genotype imputation was done with the population-specific .
The reference panel variant call set was produced with the GATK HaplotypeCaller algorithm by following GATK best practices for variant calling.
Genotype-, sample- and variant-wise QC was carried out iteratively by using the and the resulting high-quality WGS data for 8,554 individuals were phased with as described in the previous section.
Genotype imputation was carried out by using the population-specific SISu v4.2 imputation reference panel with (version 27Jan18.7e1) as described in the following protocol: .
Post-imputation quality control involved checking the expected conformity of the imputation INFO-value distribution, MAF differences between the target dataset and the imputation reference panel and checking chromosomal continuity of the imputed genotype calls.