First select the appropriate Variant Caller Parameter Settings radio button. Your radio button selection loads the correct set of default parameters for that type of run. If you want to customize parameters further, change parameter values in the main settings area. Advanced users can also click the Show Advanced Settings button to change values in the advanced settings.

These notes apply to the Variant Caller Parameter Settings and advanced settings selections:

• If you do customize settings in the advanced settings area, your changes are overwritten if you select a different Variant Caller Parameter Settings radio button (or again click on the same radio button).

• If you make changes in the advanced settings and later want to reset these parameters to their default values, again click your Variant Caller Parameter Settings radio button selection.