To run the Remove variants outside targeted regions, go to the toolbox:
Toolbox | Remove Variants () | Remove variants outside targeted regions ()
Select the track you wish to filter and click on the button labeled Next to specify the track of overlapping annotations (see figure 24.4).
Next, select the track that should be used for comparison and tick whether you wish to keep annotations that overlap, or whether to keep annotations that do not overlap with the selected track. An overlap has a simple definition - if the annotation used as input has at least one shared position with the other track, there is an overlap. The boundaries of the annotations do not need to match.