HLA-MA: simple yet powerful matching of samples using HLA typing results

Abstract

Summary: We propose the simple method HLA-MA for consistency checking in pipelines operating on human HTS data. The method is based on the HLA typing result of the state-of-the-art method OptiType. Provided that there is sufficient coverage of the HLA loci, comparing HLA types allows for simple, fast and robust matching of samples from whole genome, exome and RNA-seq data. Our approach uses information from small but genetically highly variable regions and thus complements approaches that rely on genome or exon-wide variant profiles.

Availability and implementation: The software is implemented In Python 3 and freely available under the MIT license at https://github.com/bihealth/hlama and via Bioconda.

Contact: dieter.beule@bihealth.de.

Supplementary information: Supplementary data are available at Bioinformatics online.