ArticleBioinformatics advances2022
TOSCA: an automated Tumor Only Somatic CAlling workflow for somatic mutation detection without matched normal samples.
Article in Bioinformatics advances, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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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
6 citing papers in PubMed.
- Somatic likelihood tiering: an interpretable post-calling triage protocol for tumor-only whole-exome variant review.Briefings in bioinformatics · 2026Article
- GATES: A Lightweight Tool Automating Pathogenic Variant Discovery From Raw Whole-Exome Sequencing Data.Cancer informatics · 2026Article
- ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling.Nature communications · 2025Article
- A pan-cancer atlas of therapeutic T cell targets.bioRxiv : the preprint server for biology · 2025Article
- HSP and CD279 gene expression as candidate biomarkers in symptomatic LGLL patients.Discover oncology · 2024Article
- Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery.NAR genomics and bioinformatics · 2024Article
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
Motivation: Accurate classification of somatic variants in a tumor sample is often accomplished by utilizing a paired normal tissue sample from the same patient to enable the separation of private germline mutations from somatic variants. However, a paired normal sample is not always available, making a reliable somatic variant calling more challenging. Results: To address these limitations, we developed TOSCA, the first automated tumor-only somatic calling workflow in whole-exome sequencing and targeted panel sequencing data which performs an end-to-end analysis from raw read files, via quality checks, alignment and variant calling to functional annotation, databases filtering, tumor purity and ploidy estimation and variant classification. Application of our workflow to tumor-only data provides estimates of somatic and germline variants that are consistent with results from paired analyses. Availability and implementation: TOSCA is a Snakemake-based workflow and freely available at https://github.com/mdelcorvo/TOSCA. Supplementary information: Supplementary data are available at
Identifiers
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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.