Configure the variantCaller plugin to run as part of a Planned Run

Variants are called for each barcode that is configured to use the specific reference genome, target regions file, and hotspot file that is included in the Planned Run. For more information, see Plan step in the workflow bar. When you configure the variantCaller plugin in a Planned Run, you cannot change the reference genome, target regions file, or hotspots file for any barcoded sample. The Planned Run uses the same parameter file for all barcodes.

You can configure the barcodes and set the variantCaller plugin to run automatically as part of a Planned Run in Torrent Suite™ Software.

If the variantCaller plugin runs automatically, you can run the plugin again manually after a sequencing run is completed.

IMPORTANT! The variantCaller plugin parameter settings are saved in Planned Run templates but are not saved in Planned Runs. Parameter changes that you make in a Planned Run affect only that specific run. When you change variantCaller plugin parameter settings in a Planned Run template, your changes affect all users who create Planned Runs from that template.

  1. In the Plan tab, click Templates, then select a research application in the left navigation menu.
  2. Select an existing Planned Run template from the list. Alternatively, select Add New Template, or Plan New Run to create a new Planned Run template or Planned Run.
  3. Click Plugins in the workflow bar.
  4. Select variantCaller plugin, then click Configure.

    The variantCaller plugin parameter settings change according to the selections you make. Default settings can be different depending on the sequencer in use.

  5. Select settings that are appropriate for the sequencing instrument that is used, the experiment, and the frequency of the variants of interest. For more information, see variantCaller plugin configuration.
  6. Click Next, or another tab in the workflow bar to make further changes to your Planned Run.
  7. When all changes to the Planned Run have been made, click Plan in the workflow bar, then click Plan Run.

The plugin is now set to run after every sequencing run that uses the Planned Run template or new Planned Run.

Related Topics
Parent topic: Run the variantCaller plugin