DROPS

Document

DOI: 10.4230/LIPIcs.WABI.2022.19

Pangenomic Genotyping with the Marker Array

Authors: Taher Mun, Naga Sai Kavya Vaddadi, and Ben Langmead

Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)

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.

Cite as

Taher Mun, Naga Sai Kavya Vaddadi, and Ben Langmead. Pangenomic Genotyping with the Marker Array. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 19:1-19:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

Copy BibTex To Clipboard

@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/entities/document/10.4230/LIPIcs.WABI.2022.19},
  URN =		{urn:nbn:de:0030-drops-170530},
  doi =		{10.4230/LIPIcs.WABI.2022.19},
  annote =	{Keywords: Sequence alignment indexing genotyping}
}

Search Results

Documents authored by Mun, Taher

Pangenomic Genotyping with the Marker Array

Abstract

Cite as

Thanks for your feedback!

Could not send message