What is Oncotator?

Oncotator is a web application for annotating human genomic point mutations and indels with data relevant to cancer researchers. Annotations are aggregated from the following resources:

Genomic Annotations

  • Gene, transcript, and functional consequence annotations using GENCODE for hg19.
  • Reference sequence around a variant.
  • GC content around a variant.
  • Human DNA Repair Gene annotations from Wood et al.

Protein Annotations

  • Site-specific protein annotations from UniProt.
  • Functional impact predictions from dbNSFP.

Cancer Variant Annotations

Non-Cancer Variant Annotations

Please see the help page for detailed information regarding all annotations.

Latest News

27 March 2015

Oncotator update

We’ve updated the version of Oncotator we’re using from v1.3.1.0 to v1.5.3.0. This update comes with many improvements and bug fixes to Oncotator’s annotation engine, most notably improved transcript selection. For a full list of changes, see our release page.

Get Started

Upload your input data below. Please note, only GRCh37/hg19 coordinates are supported and there is a maximum of 5,000 alterations per input file. If you need additional help, please visit our help page or feel free to contact us directly.

Upload Mutations

Upload TSV file of mutations in Oncotator format.

Paste Mutations

Paste data in Oncotator format or use example.

Web service API

Explore Oncotator's API.


Download and installation instructions