Apply a copy number baseline workflow preset to an analysis workflow

When you want to identify copy number variants (CNVs), you can select a copy number baseline to apply to the analysis workflow. These baselines are controls that you can apply to analysis workflows to determine copy number changes in the sample of interest, without the use of a matched control. You can apply a copy number baseline control only to DNA, aneuploidy, and some Oncomine™ analysis workflows.

IMPORTANT! When importing a custom copy number baseline, the target regions file used to generate the baseline must be present in the software; otherwise, the baseline is not shown in the list of available sequence variant baselines. When you add the baseline to an analysis workflow, the same target regions files that is used to create the baseline must also be used in the analysis workflow.

In the Workflows tab, start to create or copy an analysis workflow.
- Click Overview, then select an analysis workflow to copy, then click ActionsCopy.
- Click Create.
In the Reference workflow bar step, select the target regions file that was used to previously create the baseline.
The target regions file used to generate the copy number baseline must be present in the software for the imported baseline to be shown in the list of available copy number baselines.
Only baselines that were created with the same target regions file that is selected in the Reference step of the workflow bar are available.

In the Copy Number workflow bar step, select the baseline.


Option	Description
No Baseline–Don't call CNVs	If you do not want to identify CNVs, select this option.
Copy number baselines	Select an existing copy number baseline from the list.

Make a choice to view details for the baseline in the Summary pane.

Alternatively, you can click the Workflow Presets link, then configure a new copy number baseline preset. For more information, see Create a Variability Correction Informatics Baseline (VCIB) workflow preset.

Click Next.
Proceed through the remaining steps in the workflow bar.

For more information, see Steps in analysis workflow creation.
In the Confirm step, click Save Workflow.