ArticleScientific reports2023
Simple combination of multiple somatic variant callers to increase accuracy.
Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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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.
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Who cites it
12 citing papers in PubMed.
- T-rex: standardized analysis of germline variants in whole-exome sequencing trios.Scientific reports · 2026Article
- ChoCallate: a computational pipeline for consensus germline variant calling in genomic sequencing data.PeerJ · 2026Article
- Article
- Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data.Biomolecules · 2025Article
- Personalizing DNA Cancer Vaccines.Journal of personalized medicine · 2025Review
- Predicting high confidence ctDNA somatic variants with ensemble machine learning models.Scientific reports · 2025Article
- Identifying genetic errors of immunity due to mosaicism.The Journal of experimental medicine · 2025Review
- Benchmarking long-read structural variant calling tools and combinations for detecting somatic variants in cancer genomes.Scientific reports · 2025Article
- A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing.Briefings in bioinformatics · 2024Article
- Molecular targets and strategies in the development of nucleic acid cancer vaccines: from shared to personalized antigens.Journal of biomedical science · 2024Review
- Tumor Neoepitope-Based Vaccines: A Scoping Review on Current Predictive Computational Strategies.Vaccines · 2024Article
- Mutational signature assignment heterogeneity is widespread and can be addressed by ensemble approaches.Briefings in bioinformatics · 2023Article
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
No grant is acknowledged in the PubMed record.
Abstract
Publications comparing variant caller algorithms present discordant results with contradictory rankings. Caller performances are inconsistent and wide ranging, and dependent upon input data, application, parameter settings, and evaluation metric. With no single variant caller emerging as a superior standard, combinations or ensembles of variant callers have appeared in the literature. In this study, a whole genome somatic reference standard was used to derive principles to guide strategies for combining variant calls. Then, manually annotated variants called from the whole exome sequencing of a tumor were used to corroborate these general principles. Finally, we examined the ability of these principles to reduce noise in targeted sequencing.
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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.