Remove variants outside targeted regions
The overlap filter will be used to filter an annotation track based on an 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 variant results to only cover a subset of genes as explained in Select Genes by Name. Please note that for comparing variant tracks, more specific filters should be used (see Add information to variants).
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 28.3).
Figure 22.4: Select overlapping annotations track.
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.