Apply a 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! If you import a custom copy number baseline, the target regions file that was used to create the CNV baseline must be available in the software. The imported baseline then appears in the list of available copy number baselines.

  1. In the Workflows tab, start to create or copy an analysis workflow.
    • Click Overview, then select an analysis workflow to copy, then click Actions > Copy.

    • Click Create.

  2. In the Copy Number workflow bar step, select an option from the Baseline dropdown list.

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

    Note: The target regions file that was used to create the copy number baseline must be available in the software to ensure that the imported copy baseline appears 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.

    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.

    Alternatively, you can click the Workflow Presets link, then configure a new copy number baseline preset. For more information, see Create a copy number baseline workflow preset.

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

    For more information, see Steps in analysis workflow creation.

  5. In the Confirm step, click Save Workflow.