ArticleNature communications2012
A fast and accurate SNP detection algorithm for next-generation sequencing data.
Article in Nature communications, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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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.
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Who cites it
22 citing papers in PubMed.
- Article
- PAM-Independent CRISPR-Cas12a System for Specific Assays of Single Nucleotide Variants.JACS Au · 2025Article
- Genetic variation and molecular profiling of congenital malformations of the female genital tract based on whole-genome sequencing.World journal of pediatrics : WJP · 2024Article
- CannSeek? Yes we Can! An open-source single nucleotide polymorphism database and analysis portal forGigaByte (Hong Kong, China) · 2024Article
- DETexT: An SNV detection enhancement for low read depth by integrating mutational signatures into TextCNN.Frontiers in genetics · 2022Article
- Evaluation of variant calling tools for large plant genome re-sequencing.BMC bioinformatics · 2020Article
- A Fast and Scalable Workflow for SNPs Detection in Genome Sequences Using Hadoop Map-Reduce.Genes · 2020Article
- Views on GWAS statistical analysis.Bioinformation · 2020Article
- Computational Prediction and Validation of Tumor-Associated Neoantigens.Frontiers in immunology · 2020Review
- Dependency Between Protein-Protein Interactions and Protein Variability and Evolutionary Rates in Vertebrates: Observed Relationships and Stochastic Modeling.Journal of molecular evolution · 2019Article
- Identification of Quantitative Trait Loci Associated with Nutrient Use Efficiency Traits, Using SNP Markers in an Early Backcross Population of Rice (International journal of molecular sciences · 2019Article
- Application of Computational Biology and Artificial Intelligence Technologies in Cancer Precision Drug Discovery.BioMed research international · 2019Review
- Genotyping of Multiple Clinical Samples with a Combined Direct PCR and Magnetic Lateral Flow Assay.iScience · 2018Article
- High-Density Genetic Map Construction and Stem Total Polysaccharide Content-Related QTL Exploration for Chinese EndemicFrontiers in plant science · 2018Article
- A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data.Computational and structural biotechnology journal · 2018Review
- UpSetR: an R package for the visualization of intersecting sets and their properties.Bioinformatics (Oxford, England) · 2017Article
- New approaches for characterization of the genetic stability of vaccine cell lines.Human vaccines & immunotherapeutics · 2017Review
- Rising Strengths Hong Kong SAR in Bioinformatics.Interdisciplinary sciences, computational life sciences · 2017Review
- Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller.BMC genomics · 2017Article
- SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations.BMC systems biology · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Various methods have been developed for calling single-nucleotide polymorphisms from next-generation sequencing data. However, for satisfactory performance, most of these methods require expensive high-depth sequencing. Here, we propose a fast and accurate single-nucleotide polymorphism detection program that uses a binomial distribution-based algorithm and a mutation probability. We extensively assess this program on normal and cancer next-generation sequencing data from The Cancer Genome Atlas project and pooled data from the 1,000 Genomes Project. We also compare the performance of several state-of-the-art programs for single-nucleotide polymorphism calling and evaluate their pros and cons. We demonstrate that our program is a fast and highly accurate single-nucleotide polymorphism detection method, particularly when the sequence depth is low. The program can finish single-nucleotide polymorphism calling within four hours for 10-fold human genome next-generation sequencing data (30 gigabases) on a standard desktop computer.
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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.