Toolbox | Track Tools () | Annotate and Filter | Filter against Overlapping Annotations
Select the track you want to filter and click Next to specify the track of overlapping annotations (see figure 24.12).
At the top, you select the track that should be used for comparison. At the bottom you decide whether to keep annotations that overlap, or whether to keep annotations that do not overlap with the track selected. An overlap has a simple definition - if the annotation used as input has at least shares one position with the other track, there is an overlap. The boundaries of the annotation do not need to match.