Variant calling in polyploids for population and quantitative genetics
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Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study polyploid species. The genome-wide coverage and greater marker density provided by WGS data, compared to popular reduced-representation sequencing approaches, 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, like allelic dosage uncertainty, homology between subgenomes, and variance in chromosome inheritance mode, in variant calling 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.