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ACCESS Data Analysis

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​
​

Next - Setup

Installation

Last modified 2mo ago