ArticleGenome research2022
Benchmarking small-variant genotyping in polyploids.
Article in Genome research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed.
- A k-mer-based genome-wide association study approach empowering gene mining in polyploids.Nature genetics · 2026Article
- Benchmarking long-read variant calling in diploid and polyploid genomes: insights from human and plants.BMC genomics · 2026Article
- Single-Cell Genomics and Somatic Variation in Circulating and Cardiac Resident Cells.Circulation research · 2026Review
- ChoCallate: a computational pipeline for consensus germline variant calling in genomic sequencing data.PeerJ · 2026Article
- Accelerate the discovery of genetic variants in mitochondrial diseases with Variant prIOritization using Latent spAce.Briefings in bioinformatics · 2025Article
- AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids.Plant methods · 2025Article
- Genotyping short tandem repeats across copy number alterations, aneuploidies, and polyploid organisms.Communications biology · 2025Article
- Genome analyses and breeding of polyploid crops.Nature plants · 2025Review
- High-fidelity PAMless base editing of hematopoietic stem cells to treat chronic granulomatous disease.Science translational medicine · 2024Article
- Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids.The plant genome · 2023Article
- A comparison of high-throughput SARS-CoV-2 sequencing methods from nasopharyngeal samples.Scientific reports · 2022Article
- Ongoing transposition in cell culture reveals the phylogeny of diverse Drosophila S2 sublines.Genetics · 2022Article
- Variant calling in polyploids for population and quantitative genetics.Applications in plant sciencesArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Genotyping from sequencing is the basis of emerging strategies in the molecular breeding of polyploid plants. However, compared with the situation for diploids, in which genotyping accuracies are confidently determined with comprehensive benchmarks, polyploids have been neglected; there are no benchmarks measuring genotyping error rates for small variants using real sequencing reads. We previously introduced a variant calling method, Octopus, that accurately calls germline variants in diploids and somatic mutations in tumors. Here, we evaluate Octopus and other popular tools on whole-genome tetraploid and hexaploid data sets created using in silico mixtures of diploid Genome in a Bottle (GIAB) samples. We find that genotyping errors are abundant for typical sequencing depths but that Octopus makes 25% fewer errors than other methods on average. We supplement our benchmarks with concordance analysis in real autotriploid banana data sets.
Indexed as
Identifiers
What OpenQuestion holds
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.