Genotype imputation

Genotype imputation was done with the population-specific SISu v3 reference panel .

Variant call set was produced with GATK HaplotypeCaller algorithm by following GATK best-practices for variant calling.

Genotype-, sample- and variant-wise QC was applied in an iterative manner by using the Hail framework v0.1 and the resulting high-quality WGS data for 3,775 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 v3 imputation reference panel with Beagle 4.1 (version 08Jun17.d8b) as described in the following protocol: dx.doi.org/10.17504/protocols.io.nmndc5e.

Post-imputation quality-control involved checking 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.