HLA Typing from Short-Read Sequencing Data with OptiType

Abstract

The established standards for HLA genotyping rely on targeted DNA sequencing techniques. However, the increasing abundance of short-read sequencing data has prompted a demand for computational tools capable of HLA typing from general purpose sequencing data as well. OptiType is a software that performs HLA typing from short-read DNA and RNA sequencing data, and this chapter guides the user through its installation and usage.

Keywords: Bioinformatics; HLA class I typing; In silico; Mapping; OptiType; RNA-Seq; Whole-exome Seq.