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

Item Type:Article
Title:HLA-MA: simple yet powerful matching of samples using HLA typing results
Creators Name:Messerschmidt, C. and Holtgrewe, M. and Beule, D.
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: The software is implemented In Python 3 and freely available under the MIT license at https://github.com/bihealth/hlama and via Bioconda.
Keywords:Histocompatibility Testing, Sequence Analysis, DNA, Software
Source:Bioinformatics
ISSN:1367-4803
Publisher:Oxford University Press (U.K.)
Volume:33
Number:14
Page Range:2241-2242
Date:15 July 2017
Official Publication:https://doi.org/10.1093/bioinformatics/btx132
PubMed:View item in PubMed
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URLURL Type
https://edoc.mdc-berlin.de/16854/Preprint version

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