Genotype imputation

Genotype imputation was done with the population-specific SISu v4.2 reference panel.

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 Hail framework v0.2 and the resulting high-quality WGS data for 8,554 individuals were phased with Eagle 2.3.5 as described in the previous section.

Genotype imputation was carried out by using the population-specific SISu v4.2 imputation reference panel with Beagle 4.1 (version 27Jan18.7e1) as described in the following protocol: dx.doi.org/10.17504/protocols.io.xbgfijw.

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.