The imputation was done using the ImputePipelinePlugin of the PHG (PHG Wiki). The ImputePipelinePlugin was run with minRead=0 so that all haplotypes are imputed. PHG Version 0.0.40 was used to run the ImputePipelinePlugin.
Converting Illumina Infinium before imputation
Illumina data is saved in the T3 database as Ref = A_allele, Alt = B_allele. To impute this data and merge with other genotype protocols it is necessary to convert the Illumina so that it aligns (strand and orientation) with the reference genome.