This is a Preprint and has not been peer reviewed. The published version of this Preprint is available: https://doi.org/10.1002/aps3.11607. This is version 2 of this Preprint.
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Abstract
Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study polyploid species. Compared to popular reduced-representation sequencing approaches, the genome-wide coverage and greater marker density provided by WGS data can greatly improve our understanding of polyploid species and polyploid biology. However, biological features that make polyploid species interesting also pose challenges in read mapping, variant identification, and genotype estimation. Accounting for characteristics in variant calling like allelic dosage uncertainty, homology between subgenomes, and variance in chromosome inheritance mode can reduce errors. Here, I discuss the challenges of variant calling in polyploid WGS data and discuss where potential solutions can be integrated into a standard variant calling pipeline.
DOI
https://doi.org/10.32942/X2QK7N
Subjects
Life Sciences
Keywords
polyploidy, variant calling, whole genome sequence, population genetics, quantitative genetics, mixed-ploidy, mixed-ploidy, Population genetics, quantitative genetics, variant calling
Dates
Published: 2024-03-15 11:52
Last Updated: 2024-07-23 00:58
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License
CC BY Attribution 4.0 International
Additional Metadata
Language:
English
Conflict of interest statement:
None
Data and Code Availability Statement:
Not applicable
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