1. Variant calling in polyploids for population and quantitative genetics
- Author
-
Phillips, Alyssa R
- Subjects
Agricultural ,Veterinary and Food Sciences ,Crop and Pasture Production ,Genetics ,Clinical Research ,Human Genome ,2.1 Biological and endogenous factors ,Generic health relevance ,mixed ploidy ,polyploidy ,population genetics ,quantitative genetics ,variant calling ,whole genome sequence ,Crop and pasture production - 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.
- Published
- 2024