ArticleG3 (Bethesda, Md.)2015
SWEEP: A Tool for Filtering High-Quality SNPs in Polyploid Crops.
Article in G3 (Bethesda, Md.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Population-specific pangenome unveils a third FAD2 gene and solves the peanut mid-oleic fatty acid mystery.Nature communications · 2025Article
- Transcriptomic analysis for the gamma-ray-induced sweetpotato mutants with altered stem growth pattern.Frontiers in genetics · 2024Article
- Promiscuous potato: elucidating genetic identity and the complex genetic relationships of a cultivated potato germplasm collection.Frontiers in plant science · 2024Article
- Demographic history inference and the polyploid continuum.Genetics · 2023Article
- CAPG: comprehensive allopolyploid genotyper.Bioinformatics (Oxford, England) · 2023Article
- Insights into the Genomic Architecture of Seed and Pod Quality Traits in the U.S. Peanut Mini-Core Diversity Panel.Plants (Basel, Switzerland) · 2022Article
- A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes.BMC bioinformatics · 2022Article
- Unraveling the Complex Hybrid Ancestry and Domestication History of Cultivated Strawberry.Molecular biology and evolution · 2021Article
- Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes.Genes · 2020Article
- Pod and Seed Trait QTL Identification To Assist Breeding for Peanut Market Preferences.G3 (Bethesda, Md.) · 2020Article
- Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut.Frontiers in genetics · 2020Article
- Genome-wide analysis of expression quantitative trait loci (eQTLs) reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato.Horticulture research · 2020Article
- A recombination bin-map identified a major QTL for resistance to Tomato Spotted Wilt Virus in peanut (Arachis hypogaea).Scientific reports · 2019Article
- Next-generation forward genetic screens: using simulated data to improve the design of mapping-by-sequencing experiments in Arabidopsis.Nucleic acids research · 2019Article
- Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus.Annals of botany · 2019Article
- Assessment of low-coverage nanopore long read sequencing for SNP genotyping in doubled haploid canola (Brassica napus L.).Scientific reports · 2019Article
- Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection.BMC genomics · 2019Article
- Machine Learning as an Effective Method for Identifying True Single Nucleotide Polymorphisms in Polyploid Plants.The plant genome · 2019Article
- pSBVB: A Versatile Simulation Tool To Evaluate Genomic Selection in Polyploid Species.G3 (Bethesda, Md.) · 2019Article
- Major QTLs for Resistance to Early and Late Leaf Spot Diseases Are Identified on Chromosomes 3 and 5 in Peanut (Frontiers in plant science · 2019Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput next-generation sequence-based genotyping and single nucleotide polymorphism (SNP) detection opens the door for emerging genomics-based breeding strategies such as genome-wide association analysis and genomic selection. In polyploids, SNP detection is confounded by a highly similar homeologous sequence where a polymorphism between subgenomes must be differentiated from a SNP. We have developed and implemented a novel tool called SWEEP: Sliding Window Extraction of Explicit Polymorphisms. SWEEP uses subgenome polymorphism haplotypes as contrast to identify true SNPs between genotypes. The tool is a single command script that calls a series of modules based on user-defined options and takes sorted/indexed bam files or vcf files as input. Filtering options are highly flexible and include filtering based on sequence depth, alternate allele ratio, and SNP quality on top of the SWEEP filtering procedure. Using real and simulated data we show that SWEEP outperforms current SNP filtering methods for polyploids. SWEEP can be used for high-quality SNP discovery in polyploid crops.
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