Create an analysis workflow that contains a copy number baseline

Ion Reporter™ Software provides a workflow bar to guide you through the process to create an analysis workflow that contains a CNV baseline workflow preset. However, we recommend that you copy an existing predefined analysis workflow, then add the CNV baseline workflow preset to the new analysis workflow.

  1. In the Workflows tab, click the Overview screen, then select an appropriate Oncomine™ analysis workflow.
  2. Click Actions > Copy, then click Next .
  3. In the Reference step, ensure that hg19 is the selected Reference, then select Target Regions, Hotspot Regions, and Fusions BED files, then click Next.
  4. In the Annotation step, select an Annotation Set from the dropdown list, then click Next.
  5. In the Filters step, select a Filter Chain from the list, then click Next.
  6. Select the baseline that you want to use from the Baseline dropdown list.
  7. Click Next.
  8. In the Plugins step, ensure that all In-Analysis plugins are deselected, then click Next.
  9. In the Final Reports step, select a Final Report Template from the list, then click Next.
  10. In the Parameters tab, review the default settings, then click Next.

    Note: Although Read Mapping parameters are exposed when you create a CNV baseline analysis workflow, it is not necessary to change any settings.

  11. 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.

Interpretation example: The following plot shows log2 ratios across the genome and highlights panel CNV IDs. The alternating blue and green color is used to distinguish between adjacent CNV IDs. The outliers data are the small pink circles. The numbers on the X axis are the chromosomes. The CNV ID names and the mean copy number call for each CNV ID are indicated above the chromosomes. This example has copy number gains on chromosome 7 and chromosome 11. The MAPD number at the top of the plot is a QC metric measuring the noisiness of the sample. A low MAPD is good. MAPD >0.5 is considered to fail QC. Below the MAPD is the BAM file name. Log2 ratios of 0 are equivalent to a copy number call of 2 (normal). If the sample was a male, you would expect to see a copy number of 1 on chromosome X.