Create a new analysis workflow

You can create a user-defined analysis workflow in Ion Reporter™ Software that is not based on an existing analysis workflow that uses predefined settings.

This procedure is typically used when creating a workflow for a user-defined Ion AmpliSeq™ and Ion AmpliSeq™ HD research panels.

  1. In the Workflows tab, click Create Workflow.

    The workflow bar opens.

  2. In the Research Application step, select the research application and sample group, then click Next.
    If you are working with a custom Ion AmpliSeq™ research panel, you can use the following research applications, depending on the type of panel, the application and the genomic endpoints.

    • AmpliSeq Germline DNA (optionally with CNV)

    • AmpliSeq Somatic DNA (optionally with CNV)

    • AmpliSeq Somatic (Fusions)

    • AmpliSeq Somatic (DNA+Fusions)

    If you are working with a custom Ion AmpliSeq™ HD research panel, see instead Copy and edit an analysis workflow template.
  3. In the Reference step, select the required files, then click Next.
  4. In the Annotation step, select an annotation set and a MyVariants database, then click Next.
  5. In the Filters step, select a filter chain, then click Next.
  6. In the Copy Number step, select a copy number baseline, then click Next.
  7. In the Exon Tile Fusion step, for analysis workflows that apply to assays that include RNA Exon Tiling, confirm that the appropriate Exon Tile Fusion Baseline for the analysis workflow is selected, then click Next.
  8. In the Plugins step, select plugins, then click Next.
  9. In the Final Report step, select the final report template, then click Next.
  10. In the Parameters step, select parameters, then click Next.
  11. In the Confirm step, name the analysis workflow, enter an optional description, then click Save Workflow.

To check that the analysis workflow was created, click the Workflows tab, then click Overview and search for the analysis workflow name. You can now use the analysis workflow to launch an analysis. For more information, see Launch an analysis. You can also optionally download the analysis results and view them visually in the cn_results.png.