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Scripts for downstream analysis plotting of 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

  • SV Incorporation

  • CNA Processing

  • Create Patient Report

  • Intermediate file structure

• Miscellaneous Utility Scripts

  • Convert CSV to MAF

  • Get cbioportal variants

  • Convert dates to days

  • Run create_report.R