For HLA allele imputation, we extracted the extended MHC region on chromosome 6 from preimputed quality checked genotypes (hg38) according to genotype array (see ‘General imputation’) with PLINK2. We performed HLA imputation on the Michigan Imputation Server55 using the four-digit, multiethnic HLA imputation reference panel59 (v.2). Like general imputation, we phased genotypes using eagle on the server. After imputation, we filtered low-quality imputation scores (R2 < 0.7) per genotype array with BCFtools (v.1.13)60. We then merged the imputed genotypes across the four genotyping arrays with BCFtools and extracted HLA alleles from the VCF file. This resulted in a total of 2,850 HLA alleles.
