Oncotator statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Oncotator
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Tool usage distribution map

This map represents all the scientific publications referring to Oncotator per scientific context
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Associated diseases

This word cloud represents Oncotator usage per disease context
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Popular tool citations

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Protocols

Oncotator specifications

Information


Unique identifier OMICS_00178
Name Oncotator
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained No

Taxon


  • Primates
    • Homo sapiens

Versioning


No version available

Maintainer


This tool is not available anymore.

Information


Unique identifier OMICS_00178
Name Oncotator
Interface Web user interface
Restrictions to use Academic or non-commercial use
Programming languages Python
Computer skills Basic
Stability Stable
Maintained No

Taxon


  • Primates
    • Homo sapiens

Maintainer


This tool is not available anymore.

Publication for Oncotator

Oncotator citations

 (52)
library_books

Whole exome sequencing of cell free DNA and circulating tumor cells in multiple myeloma

2018
Nat Commun
PMCID: 5923255
PMID: 29703982
DOI: 10.1038/s41467-018-04001-5

[…] ding decoy sequences and re-ran MuTect to filter out mutations in problematic regions. To call somatic insertions and deletions (indels), we used Strelka and annotated the mutation consequences using Oncotator. We also filtered out SSNVs and indels present in a panel of normal samples in order to filter out potential germline sites or recurrent artifactual sites. An additional filter for cfDNA and […]

library_books

An integrated clinical and genomic information system for cancer precision medicine

2018
BMC Med Genomics
PMCID: 5918454
PMID: 29697362
DOI: 10.1186/s12920-018-0347-9

[…] (variant calling format containing details of variants) and BAM (binary alignment map for aligned reads) files, which are imported to the variant annotation and prioritization module of CGIS. We used Oncotator as the main tool for annotating genomic point mutations and short indels []. Since many transcripts can be made from the same gene, transcript selection is an important issue in variant anno […]

call_split

Dissecting the Mutational Landscape of Cutaneous Melanoma: An Omic Analysis Based on Patients from Greece

2018
PMCID: 5923351
PMID: 29596374
DOI: 10.3390/cancers10040096
call_split See protocol

[…] n panel of germ-line variants associated with melanoma based on GWAS studies and established databases [,,], focusing on those found on coding regions. Annotation of all mutations was performed using Oncotator []. Significantly mutated genes among the patients were identified using MutSigCV (version 1.41) [], which ranks the genes by estimating a background mutation rate (BMR) through the number o […]

call_split

Single nucleotide variant profiles of viable single circulating tumour cells reveal CTC behaviours in breast cancer

2018
PMCID: 5928770
PMID: 29565466
DOI: 10.3892/or.2018.6325
call_split See protocol

[…] the forward and reverse reads of the tumour sample in the mutant alleles; and iii) the nearest adjacent mutant base was at least 100 bp away in the same sample. The filtered SNVs were annotated using Oncotator (), and the variant allele fraction (VAF) was calculated as follows: VAF = read counts that covered the mutant position/all read counts that covered the position for data from a single cell. […]

library_books

Genomics of a pediatric ovarian fibrosarcoma. Association with the DICER1 syndrome

2018
Sci Rep
PMCID: 5818504
PMID: 29459759
DOI: 10.1038/s41598-018-21663-9

[…] mina 1.3.4 pipeline (Illumina, CA). For variant calling, we used MuTect ver 1.1.4 in High Confidence mode (HC) for SNV and InDelocator for small insertions and deletions. Variants were annotated with Oncotator. Non-coding variants, with the exception of splice-site mutations were excluded. SNVs and InDels were further filtered by predicted protein functional impact using Combined Annotation-Depend […]

call_split

Comparative genomic analysis of esophageal squamous cell carcinoma between Asian and Caucasian patient populations

2017
Nat Commun
PMCID: 5688099
PMID: 29142225
DOI: 10.1038/s41467-017-01730-x
call_split See protocol

[…] To identify significantly mutated genes, somatic mutations were annotated using Oncotator. MutSigCV (V1.4) was applied to identify significantly mutated genes with default covariate tables. Genes with q (FDR) < 0.1 were considered to be significantly mutated. We performed surviva […]


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Oncotator institution(s)
Cancer Program, Broad Institute, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA

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