> 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/analysis/overview-of-analysis-workflow.md).

# Overview of Analysis Workflow

Short descriptions on the steps of analysis

The pipeline aims to generate uniform and useful outputs for analyst in preliminary stage of analysis.

Example command to run through the pipeline:

## [1. Compile reads](/cmo-access-data-analysis/analysis/compile-reads.md)

```bash
> Rscript R/compile_reads.R -m $PATH/TO/master_file.csv -o $PATH/TO/results_folder
```

## [2. Filter calls](/cmo-access-data-analysis/analysis/filter-calls.md)

```bash
> Rscript R/filter_calls.R -m $PATH/TO/master_file.csv -o $PATH/TO/results_folder
```

## [3. SV incorporation](/cmo-access-data-analysis/analysis/sv-incorporation.md)

```bash
> Rscript R/SV_incorporation.R -m $PATH/TO/manifest_file.tsv -o $PATH/TO/results_folder
```

## [4. CNA processing](/cmo-access-data-analysis/analysis/cna-processing.md)

```bash
> Rscript R/CNA_processing.R -m $PATH/TO/manifest_file.tsv -o $PATH/TO/results_folder
```

## [5. Plot all events](/cmo-access-data-analysis/analysis/overview-of-analysis-workflow.md)

```bash
> Rscript R/plot_all_events.R -m $PATH/TO/manifest_file.tsv -o $PATH/TO/results_folder
```

## [6. Generate HTML report](/cmo-access-data-analysis/analysis/overview-of-analysis-workflow.md#6-generate-html-report)

<pre class="language-bash" data-overflow="wrap"><code class="lang-bash"><strong>> Rscript ~/github/access_data_analysis/reports/create_report.R -md -t ~/github/access_data_analysis/reports/template_days.Rmd -p C-L6H8E2 -r ../results_20Jan2023/results_stringent_hc/C-L6H8E2_SNV_table.csv -tt "Melanoma" -m ../manifest_noDate_days.tsv -o C-L6H8E2_days.html -rc ../results_20Jan2023/CNA_final_call_set -d P-0022907 -ds P-0022907-T01-IM6 -dm /juno/work/ccs/shared/resources/impact/facets/all/P-00229/P-0022907-T01-IM6_P-0022907-N01-IM6/default/P-0022907-T01-IM6_P-0022907-N01-IM6.ccf.maf
</strong></code></pre>

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