awesome-cancer-variant-databases

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer and normal variants. Contributions welcome.

Cancer

Clinically-focused

• CanDL - an expert-curated database of potentially actionable driver mutations for molecular pathologists and laboratory directors to facilitate literature-based annotation of genomic testing of tumors. [web app, Download]
• CiViC - CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer. [web app, API, Download]
• DGIdb - Mining the druggable genome for personalized medicine. [web app, API, Download]
• Database of Curated Mutations (DOCM) - DoCM, the Database of Curated Mutations, is a highly curated database of known, disease-causing mutations that provides easily explorable variant lists with direct links to source citations for easy verification. [web app, API, Download]
• JAX Lab Clinical Knowledge Base - The Jackson Laboratory Clinical Knowledgebase (CKB) is a semi-automated/manually curated database of gene/variant annotations, therapy knowledge, diagnostic/prognostic information, and clinical trials related to oncology. [web app]
• MyCancerGenome - My Cancer Genome is a personalized cancer medicine knowledge resource for physicians, patients, caregivers and researchers. My Cancer Genome gives up-to-date information on what mutations make cancers grow and related therapeutic implications, including available clinical trials. [web app, API, Download, may require licensing]
• Precision Medicine KnowledgeBase (PMKB) - PMKB is organized to provide information about clinical cancer variants and interpretations in a structured way, as well as allowing users to submit and edit existing entries for continued growth of the knowledgebase. All changes are reviewed by cancer pathologists. [web app, Download]

Catalogs

• COSMIC: Catalogue of Somatic Mutations in Cancer
  • downloads: http
• ISB Cancer Genomics Cloud Pilot Bigquery Table for TCGA [Web database, export as csv, json, etc.]

Germline

• dbSNP - [Web app, API, Download]
• Exome Aggregation Consortium - [Web app, API, Download]
• 1000 Genomes - [Web app, API, Download]
• ClinVar
  • downloads: ftp
• Exome Sequencing Project
  • downloads: http
  • samples: about 6500
• Genome of the Netherlands
  • downloads: http
  • samples: About 800
• UK10K
  • downloads: ftp
  • samples: About 2000
• GEUVADIS: Genetic European Variation in Health and Disease
  • downloads: ftp
  • samples: about 900
• Kaviar - Kaviar (~Known VARiants) is a compilation of SNVs, indels, and complex variants observed in humans, designed to facilitate testing for the novelty and frequency of observed variants. Kaviar contains 162 million SNV sites (including 25M not in dbSNP) and incorporates data from 35 projects encompassing 77,781 individuals (13.2K whole genome, 64.6K exome). - [web app, API, Download]
• SweGen - [Web app, API, Download]