If a target region file or hotspot file is provided to the plugin:

• Targeted regions Analysis is restricted to only the regions of interest that you specify in this file. If a targeted regions file is not provided, the variantCaller plugin will go over every position of the reference genome, which typically takes longer.

• Hotspots Variant Caller output files include these positions whether or not a variant is called, and include evidence for a variant and the filtering thresholds that disqualified a variant candidate.