ATHLATES is a software package for determining HLA genotypes for individuals from Illumina exome sequencing data. ATHLATES has been tested with 101 base paired end reads using standard whole exome kits but should be applicable to any paired sequencing of similar or greater length and accuracy that covers the HLA exons with sufficient depth (including whole genome shotgun and RNA-Seq data).
Chang Liu, Xiao Yang, Brian Duffy, Thalachallour Mohanakumar, Robi D. Mitra, Michael C. Zody, and John D. Pfeifer. ATHLATES: accurate typing of human leukocyte antigen through exome sequencing. Nucleic Acids Res 2013 Jun 8.