Step 1: Download

The download step is the first step of the Biomuta pipeline. Files containing mutations are gathered directly from the four resouces:

• The Cancer Genome Atlas (TCGA) : https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga

• International Cancer Genome Consortium (ICGC) : https://dcc.icgc.org/

• Clinical Interpretation of Variants in Cancer (CIVIC) : https://civicdb.org/welcome

• Catalogue of Somatic Mutations in Cancer (COSMIC) : https://cancer.sanger.ac.uk/cosmic

See the individual resource pages for details on the download:

• Download: TCGA
  • Fields
  • Studies
  • Downloading through Big Query
    • Step 1 - Gain All Access Requiremenets
    • Step 2 - Run downloader R script using R Studio
  • Additional Information
• Download: CIVIC
  • Fields
• Download: COSMIC
  • Fields
• Download: ICGC
  • Fields