Create an analysis workflow that contains a copy number baseline
IMPORTANT! The Target Regions and Hotspot Regions files that are used in an analysis workflow must each have a unique file name. To review the file names in the Workflows tab, go to and review the names of the hotspots files. If any of the names are identical to the Target Regions that is to be added to the analysis workflow, delete the entry in the list and upload a renamed version of the Hotspot Regions file.
Ion Reporter™ Software provides a workflow bar to guide you through the process to create or copy an analysis workflow that contains a Germline (CNV Informatics Baseline) or Somatic (CNV VCIB) workflow preset.
- In the Workflows tab, click the Overview screen, then select an appropriate Oncomine™ analysis workflow.
- Click , then click Next .
- In the Reference step, select the applicable Reference, then select the Target Regions, Hotspot Regions, and Fusions BED files, if needed, then click Next.
- In the Annotation step, select an Annotation Set from the dropdown list, then click Next.
- In the Filters step, select a Filter Chain from the list, then click Next.
- Select the baseline that you want to use from the Baseline dropdown list.
- Click Next.
- In the Plugins step, ensure that all In-Analysis plugins are deselected, then click Next.
- In the Final Reports step, select a Final Report Template from the list, then click Next.
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In the Parameters tab, review the default settings, then click Next.
Note: Although Read Mapping parameters are exposed when you create an analysis workflow that includes a VCIB baseline, it is not necessary to change any settings.
- In the Confirm tab, enter a Workflow Name and description, then click Save Workflow.
You can now use the analysis workflow to launch an analysis. For more information, see Launch an analysis. Alternatively, you can download the analysis results and view them visually in the cn_results.png. For more information, see Visualize an analysis workflow that contains a CNV baseline.