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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

SV Incorporation

  • CNA Processing

  • Create Patient Report - Single

  • Create Patient Report - Batch

  • Intermediate file structure

  • VAF Overview Plot

  • Swimmer Plot

  • Convert dates to days

    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