3.11.6. Annotate Overlapping Regions

This algorithm annotates against regions in the selected source. This algorithm identifies regions that overlap corresponding regions in the annotation source.

Requirements

An annotation source to use for annotating the regions or variants.

Options

The user may specify the following options:

  • Minimum similarity coefficient threshold is met: Matching annotation regions selected based on the specified minimum similarity coefficient

  • Current record is completely within annotation record: Matching annotation region selected if the current record is completely within the annotation record

  • Current record completely contains annotation record: Matching annotation region selected if the current record completely contains the annotation record

Output

The output includes columns for the selected source. If multiple features match the CNV then the results will be joined together in a list for each field. If a CNV does not have an overlapping feature the fields will be filled in with missing values.

The following additional fields are also included in the output:

  • # Matched: The number of events overlapping this region.

  • Region: The genomic position of the region.

  • Similarity Coefficient: The similarity of the two overlapping regions, defined as the size of the intersection divided by the size of the union, also known as the Jaccard index.

  • Overlap Type: Specifies the way in which the first region overlaps the second region. Either “Contains Region”, “Within Region”, “Identical”, or “Partial Overlap”.