hla-mapper 4

The polymorphic nature of most of the HLA and KIR genes and the high sequence similarity leads to read mapping bias and genotyping errors.

hla-mapper was designed to minimize these issues. Based on a database of known HLA and KIR 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 suites 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:
The zip file contains precompiled binaries for MacOs and Linux 64bit. 

Current version: 4.1.0
Current database version for HLA: 004.1
Current database version for KIR: 004.1

Download hla-mapper
Precompiled binaries  Download
database version 004.1 (for HLA genes)    Download
database version 004.1 (for KIR genes) (available upon request)
manual  Download

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

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