ArticlePloS one2016
Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
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Who cites it
101 citing papers in PubMed.
- An alignment-free strategy for circulating tumor DNA detection and tumor fraction estimation from whole-genome sequencing data.PLoS computational biology · 2026Article
- Benchmarking genomic variant calling tools in inbred mouse strains: recommendations and considerations.Genetics · 2026Article
- Accurate detection of tumor clonality and ongoing expansion mode from genomic data.bioRxiv : the preprint server for biology · 2026Article
- Improved tumor-only variant calling and mutation burden estimation with VarNet-T.Nature communications · 2026Article
- Synth4bench: generating synthetic data for benchmarking tumor-only somatic variant calling algorithms.Frontiers in bioinformatics · 2026Article
- A five-gene mitochondria-associated prognostic signature for bladder cancer.International journal of clinical and experimental pathology · 2026Article
- Clinical and analytical validation of a combined RNA and DNA exome assay across a large tumor cohort.Communications medicine · 2025Article
- Prediction of lung adenocarcinoma prognosis and clinical treatment efficacy by telomere-associated gene risk model.Discover oncology · 2025Article
- UNISOM: Unified Somatic Calling and Machine Learning-based Classification Enhance the Discovery of CHIP.Genomics, proteomics & bioinformatics · 2025Article
- Identifying genetic errors of immunity due to mosaicism.The Journal of experimental medicine · 2025Review
- A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing.Briefings in bioinformatics · 2024Article
- Genomic Insights into Idiopathic Granulomatous Mastitis through Whole-Exome Sequencing: A Case Report of Eight Patients.International journal of molecular sciences · 2024Article
- A Novel Affordable and Reliable Framework for Accurate Detection and Comprehensive Analysis of Somatic Mutations in Cancer.International journal of molecular sciences · 2024Article
- DEEPOMICS FFPE, a deep neural network model, identifies DNA sequencing artifacts from formalin fixed paraffin embedded tissue with high accuracy.Scientific reports · 2024Article
- Advancing bladder cancer management: development of a prognostic model and personalized therapy.Frontiers in immunology · 2024Article
- Integration of single-cell and bulk RNA-sequencing to analyze the heterogeneity of hepatocellular carcinoma and establish a prognostic model.Cancer reports (Hoboken, N.J.) · 2024Article
- Performance analysis of conventional and AI-based variant callers using short and long reads.BMC bioinformatics · 2023Article
- Oligodontia in the Clinical Spectrum of Syndromes: A Systematic Review.Dentistry journal · 2023Review
- Evaluating the performance of low-frequency variant calling tools for the detection of variants from short-read deep sequencing data.Scientific reports · 2023Article
- Technological and computational approaches to detect somatic mosaicism in epilepsy.Neurobiology of disease · 2023Review
41 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next generation sequencing is extensively applied to catalogue somatic mutations in cancer, in research settings and increasingly in clinical settings for molecular diagnostics, guiding therapy decisions. Somatic variant callers perform paired comparisons of sequencing data from cancer tissue and matched normal tissue in order to detect somatic mutations. The advent of many new somatic variant callers creates a need for comparison and validation of the tools, as no de facto standard for detection of somatic mutations exists and only limited comparisons have been reported. We have performed a comprehensive evaluation using exome sequencing and targeted deep sequencing data of paired tumor-normal samples from five breast cancer patients to evaluate the performance of nine publicly available somatic variant callers: EBCall, Mutect, Seurat, Shimmer, Indelocator, Somatic Sniper, Strelka, VarScan 2 and Virmid for the detection of single nucleotide mutations and small deletions and insertions. We report a large variation in the number of calls from the nine somatic variant callers on the same sequencing data and highly variable agreement. Sequencing depth had markedly diverse impact on individual callers, as for some callers, increased sequencing depth highly improved sensitivity. For SNV calling, we report EBCall, Mutect, Virmid and Strelka to be the most reliable somatic variant callers for both exome sequencing and targeted deep sequencing. For indel calling, EBCall is superior due to high sensitivity and robustness to changes in sequencing depths.
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