Schematic of the HLA Caller Algorithm. The HLA calling algorithm determines the most likely pair of HLA types at each locus by systematically evaluating all possible pairs of 4-digit HLA types. A) The genotyping algorithm within the GATK calculates the probability of observing particular genotypes in the data given a pair of HLA alleles. Probabilities were combined multiplicatively across base positions to obtain the cumulative probability based on genotypes. B) A binomial distribution function was used to calculate of probability of observing particular haplotypes in the data given a pair of HLA alleles. Probabilities were combined multiplicatively across pairs of polymorphic positions to obtain the cumulative probability based phase information. C) Prior probabilities for specific allele pairs were calculated as the product of allele frequencies in a specific population. Probabilities based on genotypes, phase information, and allele frequencies were combined multiplicatively to obtain the posterior probability for each HLA allele pair.