Create and use a custom parameters setting

You can create a custom parameters setting that you can save and reuse. The custom parameters setting that you create can be used with a manual run of the variantCaller plugin. To use a customized parameter file that is designed for your customized panel or other special requirements, you must create a custom parameters setting, then run the variantCaller plugin manually with the custom parameters setting.

The parameters file in the variantCaller plugin is a JSON text file that contains the variant calling parameters that are listed in variantCaller plugin advanced parameters.

  1. In the Data tab, in the Completed Runs & Reports screen, click the report name of the run that you want to apply configuration settings to.
  2. Click Plugins > Select Plugins to Run, then in the Select a Plugin to Run dialog box, click variantCaller.
  3. In the Parameter Settings section, click Custom.

    To . . .

    Do this . . .

    Use a JSON parameters file that you have saved on your computer.

    1. Click Load external parameter file.

    2. Browse to the JSON file, then click Open.

    Edit a predefined parameters setting.

    1. In Configuration, select the predefined parameter setting that you want to edit.

    2. Click Copy selected to Custom.

    3. If you agree to save the new custom parameter setting, click OK.

    4. Click Show Advanced Settings to enter changes for the custom parameter settings.

    You can edit the values of the advanced parameter settings. Predefined parameter settings are in read-only mode and cannot be edited.

The custom parameters setting is now ready to be applied to run results when you run the variantCaller plugin manually.

Related Topics
Parent topic: Variant calls in Torrent Suite™ Software