Pangenomic Genotyping with the Marker Array

Authors Taher Mun , Naga Sai Kavya Vaddadi, Ben Langmead

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Author Details

Taher Mun
  • Johns Hopkins University, Baltimore MD, USA
  • Illumina, San Diego, USA
Naga Sai Kavya Vaddadi
  • Johns Hopkins University, Baltimore MD, USA
Ben Langmead
  • Johns Hopkins University, USA


We thank Massimiliano Rossi and Travis Gagie for many helpful discussions. We thank Margaret Gagie for her careful editing. Part of this research project was conducted using computational resources at the Maryland Advanced Research Computing Center (MARCC).

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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)


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.

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ACM Subject Classification
  • Applied computing → Computational genomics
  • Sequence alignment indexing genotyping


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