Step 2: Convert

For each resource, a unique script is used to convert from the raw format provided by the resource, to a format aligned with past versions of the Biomuta pipeline.

With a common format, all resources can then be combined into a master dataset.

See the individual resource pages for details on the conversion:

• Convert: TCGA
  • Scripts
  • Procedure
    • Run process_tcga_download.py
      • Summary
      • Script Specifications
        • Input
        • Output
        • Usage
  • Additional Notes
• Convert: CIVIC
  • Scripts
  • Procedure
    • Perform liftover of mutations from GRCh37 to GRCh38
      • Summary
    • Run convert_civic_vcf.py
      • Summary
      • Script Specifications
        • Input
        • Output
        • Usage
    • Run map_civic_csv.py
      • Summary
      • Script Specifications
        • Input
        • Output
        • Usage
  • Additional Notes
• Convert: COSMIC
  • Scripts
  • Procedure
    • Run map_cosmic_tsv.py
      • Summary
      • Script Specifications
        • Input
        • Output
        • Usage
  • Additional Notes
• Convert: ICGC
  • Scripts
  • Procedure
    • Perform liftover of mutations from GRCh37 to GRCh38 (mapvcf_copySA)
      • Summary
    • Genomic Liftover Notes
      • Fields
      • Converting with CrossMap
    • Run convert_icgc_vcf.py
      • Summary
      • Script Specifications
        • Input
        • Output
        • Usage
    • Run map_icgc.py
      • Summary
      • Script Specifications
        • Input
        • Output
        • Usage
  • Additional Notes