hla-mapper 4

The polymorphic nature of most HLA genes and their high sequence similarity lead to read mapping bias and genotyping errors. hla-mapper was designed to minimize these issues. Based on a database of known HLA sequences, each read pair is scored and addressed to the most likely locus. The final output is a BAM file with reads mapped to the human reference genome (version hg38), allowing any downstream analysis that suits the user. The resulting BAM file is far more reliable than those generated by using BWA, Bowtie2, or other mapping tools directly.

How to install:
hla-mapper is now on GitHub. 

Versions 2 and 3 has been discontinued.

How to cite hla-mapper
Hla-mapper: an application to optimize the mapping of hla sequences produced by massively parallel sequencing procedures. Human Immunology 2018. doi: 10.1016/j.humimm.2018.06.010