Filter Based on Overlap
Filter Based on Overlap takes as input a track that contains region-specific information, hereby referred to as annotations. The following track types are supported:
- Variant track (
)
- Annotation track (
)
- Expression track (
)
- Statistical comparison track (
)
The tool can be used to e.g. restrict to variants that fall within genes or regulatory regions.
To run the tool, go to:
Tools | Utility Tools (
) | Filtering (
) | Filter Based on Overlap (
)
The following options can be configured (figure 37.8):
- Track(s) At least one track, used for calculating the overlaps.
- Overlapping annotations options The content of the output track (figure 37.9). Hover the mouse cursor over the option to see an example on input and output.
- Keep overlapping annotations The annotations in the input track that overlap with any annotations in the other track(s).
- Keep overlapping annotation parts The annotations in the input track that overlap with any annotations in the other track(s), shortened to the region of the overlap. This option can only be used for annotation tracks.
- Remove overlapping annotations The annotations in the input track that do not overlap with any annotations in the other track(s).
- Remove overlapping annotation parts The annotations in the input track that do not overlap with any annotations in the other track(s), shortened to the region of no overlap. This option can only be used for annotation tracks.
Figure 37.8: The available options in Filter Based on Overlap. Hovering the mouse cursor over an overlapping annotation option reveals a tooltip with an example of input and output.
Fusions in annotation tracks produced by Detect and Refine Fusion Genes or Detect Fusion Genes from DNA are represented by two annotations, one for the 5' breakpoint and one for the 3' breakpoint. To preserve the full fusion information, filtering is applied at the fusion level, i.e., both annotations are retained or discarded together. When filtering using:
- Keep: Both annotations are included if either one satisfies the filtering criteria.
- Remove: Both annotations are excluded if either one does not satisfy the filtering criteria.
Figure 37.9: A track list with an input annotation track a and another annotation track b, as well as the output tracks from Filter Based on Overlap, using each overlapping annotations option. "Keep overlapping annotations": keep. "Keep overlapping annotation parts": keep parts. "Remove overlapping annotations": remove. "Remove overlapping annotation parts": remove parts.