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ACCESS Data Analysis

Scripts for downstream analysis and plotting of the ACCESS variant calling pipeline output

This gitbook will walk you through:

  • Setup

    • Installation

  • Master file creation
    Resource files
    Analysis
    Overview of Analysis Workflow
    Compile Reads
    Filter Calls
    Miscellaneous Utility Scripts
    Compile Reads Input Generation
    Convert CSV to MAF
    Get cbioportal variants
    SV Incorporation
    CNA Processing
    Create Patient Report - Single
    Create Patient Report - Batch
    Intermediate file structure
    VAF Overview Plot
    Swimmer Plot
    Convert dates to days