Variants and allelic frequencies HLA class I genes (SABE-1171-WGS hg38).

We applied hla-mapper in the SABE cohort (SABE-1171-WGS), a pipeline developed to optimize mappings for HLA genes, providing high-confidence genotype and haplotype calls for this unusually polymorphic region, with complex structure involving duplications. We have detected 2.4X more variants in the HLA class I genes than with the computational workflow for genotype calling in the entire genome. Many variants are multiallelic and some alternate alleles are marked as *, meaning that there is a deletion that spans that position of interest.