Pangenomic genotyping with the marker array

• Published in: Algorithms for molecular biology Vol. 18; no. 1; pp. 2 - 17
• Main Authors: Mun, Taher, Vaddadi, Naga Sai Kavya, Langmead, Ben
• Format: Journal Article
• Language: English
• Published: London BioMed Central 05.05.2023; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Algorithms; Arrays; Bias; Bioinformatics; Biomedical and Life Sciences; Cellular and Medical Topics; Computational Biology/Bioinformatics; Genetic aspects; Genomes; Genomics; Genotype & phenotype; Genotypes; Genotyping; Haplotypes; Indexing; Life Sciences; Open source software; Physiological; Polymorphism; Public software; Selected papers from WABI 2022; Sequence alignment; Software; Genotyping; Sequence alignment; Indexing
• ISSN: 1748-7188; 1748-7188
• DOI: 10.1186/s13015-023-00225-3

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 reducing 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. The method is implemented in the open source software tool rowbowt available at https://github.com/alshai/rowbowt .