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Creative Commons Attribution 4.0 International license (CC BY 4.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.WABI.2022.19
URN: urn:nbn:de:0030-drops-170530
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2022/17053/
Mun, Taher ;
Vaddadi, Naga Sai Kavya ;
Langmead, Ben
Pangenomic Genotyping with the Marker Array
Abstract
We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while avoiding the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods.
BibTeX - Entry
@InProceedings{mun_et_al:LIPIcs.WABI.2022.19,
author = {Mun, Taher and Vaddadi, Naga Sai Kavya and Langmead, Ben},
title = {{Pangenomic Genotyping with the Marker Array}},
booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)},
pages = {19:1--19:17},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-243-3},
ISSN = {1868-8969},
year = {2022},
volume = {242},
editor = {Boucher, Christina and Rahmann, Sven},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/opus/volltexte/2022/17053},
URN = {urn:nbn:de:0030-drops-170530},
doi = {10.4230/LIPIcs.WABI.2022.19},
annote = {Keywords: Sequence alignment indexing genotyping}
}
