Filter against overlapping annotations

The overlap filter will be used for filtering an annotation track based on overlap with another annotation track. This can be used to e.g. only show variants that fall within genes or regulatory regions or for restricting variants results to only cover a subset of genes as explained in Filter annotations on name. Please note that for comparing variant tracks, more specific filters should be used (see Annotate and filter from variant database).

        Toolbox | Track Tools (Image 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).

Image filter_against_overlapping_annotations_step2
Figure 24.12: Select overlapping annotations track.

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.