# Home

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

This gitbook will walk you through:

* [Setup](https://cmo-ci.gitbook.io/cmo-access-data-analysis/setup/setup-for-running-analysis)
  * [Installation](https://cmo-ci.gitbook.io/cmo-access-data-analysis/setup/installation)
  * [Master file creation](https://cmo-ci.gitbook.io/cmo-access-data-analysis/setup/setup-for-running-analysis#master-reference-file)
  * [Resource files](https://cmo-ci.gitbook.io/cmo-access-data-analysis/setup/resources)
* [Analysis](https://cmo-ci.gitbook.io/cmo-access-data-analysis/analysis/overview-of-analysis-workflow)
  * [Overview of Analysis Workflow](https://cmo-ci.gitbook.io/cmo-access-data-analysis/analysis/overview-of-analysis-workflow)
  * [Compile Reads](https://cmo-ci.gitbook.io/cmo-access-data-analysis/analysis/compile-reads)
  * [Filter Calls](https://cmo-ci.gitbook.io/cmo-access-data-analysis/analysis/filter-calls)
  * [SV Incorporation](https://cmo-ci.gitbook.io/cmo-access-data-analysis/analysis/sv-incorporation)
  * [CNA Processing](https://cmo-ci.gitbook.io/cmo-access-data-analysis/analysis/cna-processing)
  * [Create Patient Report - Single](https://cmo-ci.gitbook.io/cmo-access-data-analysis/analysis/create-report)
  * [Create Patient Report - Batch](https://cmo-ci.gitbook.io/cmo-access-data-analysis/run-create_report.r)
  * [Intermediate file structure](https://cmo-ci.gitbook.io/cmo-access-data-analysis/analysis/intermediate-file-organization)
  * [VAF Overview Plot](https://cmo-ci.gitbook.io/cmo-access-data-analysis/vaf-overview-plot-script)
  * [Swimmer Plot](https://cmo-ci.gitbook.io/cmo-access-data-analysis/swimmer-plot-scripts)
* [Miscellaneous Utility Scripts](https://cmo-ci.gitbook.io/cmo-access-data-analysis/miscellaneous-utility-scripts)
  * [Compile Reads Input Generation](https://cmo-ci.gitbook.io/cmo-access-data-analysis/manifest-update-script)
  * [Convert CSV to MAF](https://cmo-ci.gitbook.io/cmo-access-data-analysis/miscellaneous-utility-scripts/convert-csv-to-maf)
  * [Get cbioportal variants](https://cmo-ci.gitbook.io/cmo-access-data-analysis/miscellaneous-utility-scripts/get-cbioportal-variants)
  * [Convert dates to days](https://cmo-ci.gitbook.io/cmo-access-data-analysis/miscellaneous-utility-scripts/convert_dates_to_days)