ArticleBMC bioinformatics2014
Combining calls from multiple somatic mutation-callers.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Benchmarking genomic variant calling tools in inbred mouse strains: recommendations and considerations.Genetics · 2026Article
- Integrated genomic analysis of NF1-associated peripheral nerve sheath tumors: an updated biorepository dataset.Scientific data · 2025Article
- Benchmarking long-read structural variant calling tools and combinations for detecting somatic variants in cancer genomes.Scientific reports · 2025Article
- CaMutQC: An R package for integrative quality control and filtration of cancer somatic mutations.Computational and structural biotechnology journal · 2025Article
- A Novel Affordable and Reliable Framework for Accurate Detection and Comprehensive Analysis of Somatic Mutations in Cancer.International journal of molecular sciences · 2024Article
- Mutational signature assignment heterogeneity is widespread and can be addressed by ensemble approaches.Briefings in bioinformatics · 2023Article
- Simple combination of multiple somatic variant callers to increase accuracy.Scientific reports · 2023Article
- Detailed evaluation of cancer sequencing pipelines in different microenvironments and heterogeneity levels.Turkish journal of biology = Turk biyoloji dergisi · 2021Article
- SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach.Scientific reports · 2020Article
- Pan-cancer analysis of whole genomes.Nature · 2020Article
- Informatics for cancer immunotherapy.Annals of oncology : official journal of the European Society for Medical Oncology · 2017Review
- Improving somatic variant identification through integration of genome and exome data.BMC genomics · 2017Article
- In-depth comparison of somatic point mutation callers based on different tumor next-generation sequencing depth data.Scientific reports · 2016Article
- Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data.BMC bioinformatics · 2016Article
- Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data.PloS one · 2016Article
- An ensemble approach to accurately detect somatic mutations using SomaticSeq.Genome biology · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundAccurate somatic mutation-calling is essential for insightful mutation analyses in cancer studies. Several mutation-callers are publicly available and more are likely to appear. Nonetheless, mutation-calling is still challenging and there is unlikely to be one established caller that systematically outperforms all others. Therefore, fully utilizing multiple callers can be a powerful way to construct a list of final calls for one's research.
resultsUsing a set of mutations from multiple callers that are impartially validated, we present a statistical approach for building a combined caller, which can be applied to combine calls in a wider dataset generated using a similar protocol. Using the mutation outputs and the validation data from The Cancer Genome Atlas endometrial study (6,746 sites), we demonstrate how to build a statistical model that predicts the probability of each call being a somatic mutation, based on the detection status of multiple callers and a few associated features.
conclusionThe approach allows us to build a combined caller across the full range of stringency levels, which outperforms all of the individual callers.
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