| _version_ | 1867013640610119680 |
|---|---|
| author | Alyssa R. Phillips |
| author_facet | Alyssa R. Phillips Alyssa R. Phillips |
| collection | Wiley Open Access |
| contents | Variant calling in polyploids for population and quantitative genetics Alyssa R. Phillips Applications in Plant Sciences AbstractAdvancements 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. 10.1002/aps3.11607 http://creativecommons.org/licenses/by-nc/4.0/ |
| doi_str_mv | 10.1002/aps3.11607 |
| format | Artículo Open Access |
| id | wiley_oa_10_1002_aps3_11607 |
| institution | Wiley Open Access |
| license_str_mv | http://creativecommons.org/licenses/by-nc/4.0/ |
| publishDate | 2024 |
| publisher | Wiley |
| record_format | wiley_oa |
| spellingShingle | Variant calling in polyploids for population and quantitative genetics Alyssa R. Phillips Applications in Plant Sciences Variant calling in polyploids for population and quantitative genetics Alyssa R. Phillips Applications in Plant Sciences AbstractAdvancements 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. 10.1002/aps3.11607 http://creativecommons.org/licenses/by-nc/4.0/ |
| title | Variant calling in polyploids for population and quantitative genetics |
| topic | Applications in Plant Sciences |
| url | https://bsapubs.onlinelibrary.wiley.com/doi/10.1002/aps3.11607 |