ArticlePLoS genetics2016
GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data.
Article in PLoS genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Unveiling the genetic determinants of germination efficiency in common bermudagrass: A genome-wide association study.The plant genome · 2026Article
- Missing or Mis-Telling the Story? Trade-Offs for Restriction-Site Associated Compared to Whole Genome Sequencing.Molecular ecology · 2026Article
- Genome-wide association studies reveal genetic variants associated with antineoplastic monoterpenoid indole alkaloid accumulation inFrontiers in plant science · 2026Article
- Genotype imputation from low-coverage WGS using haplotype reference panels in cultivated strawberry.BMC genomics · 2025Article
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- Variant calling and genotyping accuracy of ddRAD-seq: Comparison with 20X WGS in layers.PloS one · 2024Article
- CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes.Genome research · 2023Article
- Commonly used Hardy-Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data.Molecular ecology resources · 2022Article
- Novel GBS-Based SNP Markers for Finger Millet and Their Use in Genetic Diversity Analyses.Frontiers in genetics · 2022Article
- Genome-Wide Association Study Reveals Novel Candidate Genes Associated with Productivity and Disease Resistance toG3 (Bethesda, Md.) · 2020Article
- Environment-dependent introgression from Quercus dentata to a coastal ecotype of Quercus mongolica var. crispula in northern Japan.The New phytologist · 2020Article
- Maximising recombination across macadamia populations to generate linkage maps for genome anchoring.Scientific reports · 2020Article
- Article
- Review
- Improving genomic predictions by correction of genotypes from genotyping by sequencing in livestock populations.Journal of animal science and biotechnology · 2019Article
- Ancestry informative alleles captured with reduced representation library sequencing in Theobroma cacao.PloS one · 2018Article
- Article
- How and how much does RAD-seq bias genetic diversity estimates?BMC evolutionary biology · 2016Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Reduced representation sequencing methods such as genotyping-by-sequencing (GBS) enable low-cost measurement of genetic variation without the need for a reference genome assembly. These methods are widely used in genetic mapping and population genetics studies, especially with non-model organisms. Variant calling error rates, however, are higher in GBS than in standard sequencing, in particular due to restriction site polymorphisms, and few computational tools exist that specifically model and correct these errors. We developed a statistical method to remove errors caused by restriction site polymorphisms, implemented in the software package GBStools. We evaluated it in several simulated data sets, varying in number of samples, mean coverage and population mutation rate, and in two empirical human data sets (N = 8 and N = 63 samples). In our simulations, GBStools improved genotype accuracy more than commonly used filters such as Hardy-Weinberg equilibrium p-values. GBStools is most effective at removing genotype errors in data sets over 100 samples when coverage is 40X or higher, and the improvement is most pronounced in species with high genomic diversity. We also demonstrate the utility of GBS and GBStools for human population genetic inference in Argentine populations and reveal widely varying individual ancestry proportions and an excess of singletons, consistent with recent population growth.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.