%0 Journal Article %A Alexander T Dilthey %A Pierre-Antoine Gourraud %A Zamin Iqbal %A Gil McVean %T High-accuracy HLA type inference from whole-genome sequencing data %D 2015 %R 10.1101/035253 %J bioRxiv %P 035253 %X Extensive hyperpolymorphism and sequence similarity between the HLA genes make HLA type inference from whole-genome sequencing data a challenging problem. We address these by representing sequences from over 10,000 known alleles in a reference graph structure, enabling accurate read mapping. HLA*PRG, our algorithm, outperforms existing methods by a wide margin and for the first time consistently achieves the accuracy of gold-standard reference methods with one error across 158 alleles tested. %U https://www.biorxiv.org/content/biorxiv/early/2015/12/24/035253.full.pdf