> For the complete documentation index, see [llms.txt](https://niagads.gitbook.io/vcpa/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://niagads.gitbook.io/vcpa/step-6-submit-a-job-to-process-one-whole-genome-wgs-whole-exome-wes-sample/6.2-choose-which-workflow-to-use.md).

# 6.2 Choose which workflow to use

**VCPA allows user to process either a WGS or WES sample using the latest human reference genome (hg38). For WGS, VCPA provides two options: with or without mapping. Below are the three VCPA workflow options that users can choose from:**

* **VCPA\_WES\_hg38\_from\_mapping\_to\_variant\_call.sh -**  this is the WES pipeline that includes steps from mapping to variant call using GATK (i.e. steps 0, 1, 2a and 2b in the overview figure in the Introduction session)
* **VCPA\_WGS\_hg38\_from\_mapping\_to\_variant\_call.sh -**  this is the WGS pipeline that includes steps from mapping to variant call using GATK (i.e. steps 0, 1, 2a and 2b in the overview figure in the Introduction session)
* **VCPA\_WGS\_hg38\_from\_markdup\_to\_variant\_call.sh -**  this is the WGS pipeline that excludes mapping, but includes other steps of VCPA (i.e. steps 1, 2a and 2b in the overview figure in the Introduction session)

**Users can choose the workflow by doing this:**

```
cp bin/${PROJECT_WORKFLOW}.sh bin/${PROJECT_WORKFLOW}_aws.sh
```

{% hint style="info" %}
PROJECT\_WORKFLOW is the one of the three .sh file chosen from the above.
{% endhint %}