ReviewNature reviews. Genetics2011
Genotype and SNP calling from next-generation sequencing data.
Review in Nature reviews. Genetics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 630 papers, 2 of them syntheses that pooled it.
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
630 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Pooled it
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Germline genetic variation in prostate susceptibility does not predict outcomes in the chemoprevention trials PCPT and SELECT.Prostate cancer and prostatic diseases · 2020Trial
- Identifying adaptive variation in spatially structured populations using low-coverage whole-genome sequencing data.Molecular biology and evolution · 2026Article
- Predictive evolutionary genomics: principles, validation, and practice.The New phytologist · 2026Review
- Genomic differentiation and SNP variation reveal local adaptations to eastern Mediterranean environmental conditions in wild radishes.Annals of botany · 2026Article
- Low-Coverage Whole-Genome Resequencing in Livestock and Poultry: Statistical Foundations, Applications and Future Directions.Biology · 2026Review
- Article
- Population history rather than tree age contributes to the evolutionary importance of ancient trees in an endangered conifer.Nature plants · 2026Article
- Genotypic Characterization and Evaluation ofCurrent issues in molecular biology · 2026Article
- VCboost: reducing false positives in long-read variant calling for single-nucleotide polymorphism and indel detection in challenging genomic regions.Briefings in bioinformatics · 2026Article
- Applicability and performance evaluation of the Shennong 1 chicken 40 K liquid chip in commercial chicken populations.Poultry science · 2026Article
- lcUMAPtSNE: use of non-linear dimensionality reduction techniques with genotype likelihoods.BMC genomics · 2026Article
- Fifteen Years of the Genome Analysis Toolkit as the De Facto Standard in Short-Read Variant Calling.International journal of molecular sciences · 2026Review
- Species-Specific Susceptibility of Planktonic and Biofilm Forming Candida Strains to Cyclodextrin-Encapsulated Essential Oils.Pharmaceutics · 2026Article
- AI solutions for evolutionary genomics of nonmodel species.Evolution letters · 2026Review
- Benchmarking imputation accuracy in the presence or absence of a reference panel.Molecular biology and evolution · 2026Article
- Genome-Wide Association Study Uncovers Candidate Genes Governing Oil Quality Traits in Sunflower (Plants (Basel, Switzerland) · 2026Article
- High-quality genome ofPlant diversity · 2026Article
- A novel simulation tool for low-coverage whole-genome sequencing using multivariate Gaussian mixture models.BMC bioinformatics · 2026Article
570 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and quantify the considerable uncertainty associated with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data. We review these methods and provide a guide for their use in NGS studies.
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.