> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/cmo-access-data-analysis/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/cmo-access-data-analysis/undefined.md).

# Home

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

This gitbook will walk you through:

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