RT Journal Article
SR Electronic
T1 High-accuracy HLA type inference from whole-genome sequencing data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 035253
DO 10.1101/035253
A1 Alexander T Dilthey
A1 Pierre-Antoine Gourraud
A1 Zamin Iqbal
A1 Gil McVean
YR 2015
UL http://biorxiv.org/content/early/2015/12/24/035253.abstract
AB 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.