Workflow of seq2HLA. (a) RNA-Seq reads are mapped against the reference HLA sequences. (b) For each locus, the allele with the greatest number of reads is determined. (c) Reads associated with the first determined group are removed and the mapping procedure is repeated. (d) The second digital haplotype is called. (e) Zygosity is determined. (f) The genotype and the associated P-values are reported.