ArticleNucleic acids research2011
SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 152 papers.
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Who cites it
152 citing papers in PubMed.
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- A comprehensive catalog of single nucleotide polymorphisms (SNPs) from the black pepper (Piper nigrum L.) genome.BMC genomics · 2025Article
- Novel biallelic MCMDC2 variants were associated with meiotic arrest and nonobstructive azoospermia.Asian journal of andrology · 2025Article
- The Bioinformatic Applications of Hi-C and Linked Reads.Genomics, proteomics & bioinformatics · 2024Review
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- The DNA repair pathway as a therapeutic target to synergize with trastuzumab deruxtecan in HER2-targeted antibody-drug conjugate-resistant HER2-overexpressing breast cancer.Journal of experimental & clinical cancer research : CR · 2024Article
- Clonal Hematopoiesis of Indeterminate Potential Is Associated with Current Smoking Status and History of Exacerbation in Patients with Chronic Obstructive Pulmonary Disease.Tuberculosis and respiratory diseases · 2024Article
- Genomic analyses correspond with deep persistence of peoples of Blackfoot Confederacy from glacial times.Science advances · 2024Article
- Prediction of metabolites associated with somatic mutations in cancers by using genome-scale metabolic models and mutation data.Genome biology · 2024Article
- Prognostic value of theTherapeutic advances in medical oncology · 2024Article
- Assessing the impact of sequencing platforms and analytical pipelines on whole-exome sequencing.Frontiers in genetics · 2024Article
- Systematic comparison of variant calling pipelines of target genome sequencing cross multiple next-generation sequencers.Frontiers in genetics · 2023Article
- Frequency and Functional Characterization ofHuman mutation · 2023Article
92 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
We develop a statistical tool SNVer for calling common and rare variants in analysis of pooled or individual next-generation sequencing (NGS) data. We formulate variant calling as a hypothesis testing problem and employ a binomial-binomial model to test the significance of observed allele frequency against sequencing error. SNVer reports one single overall P-value for evaluating the significance of a candidate locus being a variant based on which multiplicity control can be obtained. This is particularly desirable because tens of thousands loci are simultaneously examined in typical NGS experiments. Each user can choose the false-positive error rate threshold he or she considers appropriate, instead of just the dichotomous decisions of whether to 'accept or reject the candidates' provided by most existing methods. We use both simulated data and real data to demonstrate the superior performance of our program in comparison with existing methods. SNVer runs very fast and can complete testing 300 K loci within an hour. This excellent scalability makes it feasible for analysis of whole-exome sequencing data, or even whole-genome sequencing data using high performance computing cluster. SNVer is freely available at http://snver.sourceforge.net/.
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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.