ArticleBioinformatics (Oxford, England)2012
SomaticSniper: identification of somatic point mutations in whole genome sequencing data.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 420 papers, 1 of them a synthesis that pooled it.
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Who cites it
420 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Transformers meets neoantigen detection: a systematic literature review.Journal of integrative bioinformatics · 2024Pooled it
- Tumor ecosystem and microbiome features associated with efficacy and resistance to avelumab plus chemoradiotherapy in head and neck cancer.Nature cancer · 2026Trial
- Neoantigen-specific tumor-infiltrating lymphocytes in gastrointestinal cancers: a phase 2 trial.Nature medicine · 2025Trial
- Nilotinib in KIT-driven advanced melanoma: Results from the phase II single-arm NICAM trial.Cell reports. Medicine · 2024Trial
- Nivolumab plus ipilimumab in advanced salivary gland cancer: a phase 2 trial.Nature medicine · 2023Trial
- Integrated multi-omics analysis reveals the molecular landscape and therapeutic strategies in Chinese cervical cancer patients.PLoS biology · 2026Article
- Widespread atypical UV-induced mutations form in single-stranded DNA.Science advances · 2026Article
- TERT drives liver tumorigenesis beyond telomere elongation.Life science alliance · 2026Article
- Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic.Nature biotechnology · 2026Article
- Malignant B-cell States Orchestrate Spatially Organized Immune Ecosystems in B-cell Lymphomas.Research square · 2026Article
- ClairS: a deep-learning method for long-read tumor-normal pair somatic small variant calling.Nature methods · 2026Article
- Surveying the Genomic Landscape of Mantle Cell Lymphoma Indicates the Importance of Multimodal Genomic and Transcriptomic Exploration.medRxiv : the preprint server for health sciences · 2026Article
- SERPINH1 expression represents a reliable biomarker of human breast cancer aggressiveness.Biology direct · 2026Article
- AI-driven neoantigen identification: a comprehensive review from somatic variant calling to T cell recognition.Journal of translational medicine · 2026Review
- MRDsteer: quality-aware AI-driven closed-loop optimization enhances ctDNA-based minimal residual disease detection.Briefings in bioinformatics · 2026Article
- Patient-derived organoids across cancers reveal conserved tumor heterogeneity and actionable therapeutic vulnerabilities.Science advances · 2026Article
- VariantMedium: sensitive and generalizable somatic point mutation calling with 3D DenseNets trained and evaluated on experimental data.Genome medicine · 2026Article
- A Deep Learning-Driven Framework Integrating Organoid-Based Functional Validation Identifies Universal Neoantigens from Recurrent Glioma Mutations.Cancer research · 2026Article
- Geospatial genetic evolution and phenotypic plasticity in triple-negative breast cancer.Genome medicine · 2026Article
- Genetic attenuation of ALDH1A1 increases metastatic potential and aggressiveness in colorectal cancer.Molecular oncology · 2026Article
360 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
motivationThe sequencing of tumors and their matched normals is frequently used to study the genetic composition of cancer. Despite this fact, there remains a dearth of available software tools designed to compare sequences in pairs of samples and identify sites that are likely to be unique to one sample.
resultsIn this article, we describe the mathematical basis of our SomaticSniper software for comparing tumor and normal pairs. We estimate its sensitivity and precision, and present several common sources of error resulting in miscalls. AVAILABILITY AND IMPLEMENTATION: Binaries are freely available for download at http://gmt.genome.wustl.edu/somatic-sniper/current/, implemented in C and supported on Linux and Mac OS X. CONTACT: delarson@wustl.edu; lding@wustl.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.