# Genotype imputation

Genotype imputation was done with the population-specific [SISu v4.2 reference panel](https://finngen.gitbook.io/documentation/v/r8/methods/genotype-imputation/sisu-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](https://hail.is/) and the resulting high-quality WGS data for 8,554 individuals were phased with [Eagle 2.3.5](https://alkesgroup.broadinstitute.org/Eagle/) 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](https://faculty.washington.edu/browning/beagle/b4_1.html) (version 27Jan18.7e1) as described in the following protocol: [dx.doi.org/10.17504/protocols.io.xbgfijw](https://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.