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Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Oncotator data sources

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
edited June 2014 in Oncotator documentation

For human / cancer-related research applications, we aggregate annotations from the following resources listed below. Please note that some of these may not be publicly available. We provide a bundle of publicly available resources on our Downloads page.

Important note: these datasources now use GENCODE v19 instead of GAF 3.0 for transcript annotations, such as 'gene'. The current version of Oncotator is backward compatible with previous datasources, but moving forward, we cannot guarantee that will be the case for future versions.

Genomic Annotations

  • Gene, transcript, and functional consequence annotations using GENCODE hg19 reference set. Both basic transcripts and long noncoding RNA are provided.
  • Common SNP annotations from dbSNP (includes data from 1000 Genomes project pilot 1, 2, and 3 studies), ESP, and 1000G
  • HGVS Nomenclature support for GENCODE v19+/ENSEMBL transcripts.
  • Sequence Ontology terms

Protein Annotations

  • Site-specific protein annotations from UniProt
  • Druggable target data from DrugBank
  • Functional impact predictions from dbNSFP, which includes PolyPhen-2, SIFT, MutationAssessor, LRT, FATHMM, and more.

Cancer Annotations

Post edited by LeeTL1220 on


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