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 (Image remove_information_closed_16_n_p) | Remove variants outside targeted regions (Image remove_variants_outside_target_regions_16_n_p)

Select the track you wish to filter and click on the button labeled Next to specify the track of overlapping annotations (see figure 31.3).

Image filter_against_overlapping_annotations_step2
Figure 24.4: 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.