HDF5 format using LIMIX converter (LIMIX converter, --g012_dosage). For eQTL mapping, we included autosomal variants with a minimum minor allele frequency of 1% in our samples and maximum 10% missing values across individuals. Variant sites were further required to have a minimum IMPUTE2 INFO score of 0.4 to assure good imputation quality. Missing genotypes were mean imputed and the dosage of the alternative allele used for mapping.
