# Genotype imputation

Genotype imputation was done with the population-specific [SISu v3 reference panel ](https://finngen.gitbook.io/documentation/r4/methods/genotype-imputation/sisu-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](https://github.com/hail-is/hail) 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](https://faculty.washington.edu/browning/beagle/b4_1.html) (version 08Jun17.d8b) as described in the following protocol: [dx.doi.org/10.17504/protocols.io.nmndc5e](https://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.