3.11.5. Annotate Overlapping Genes

This algorithm identifies regions that overlap genes in the selected source.

This algorithm only performs the simple case of whether or not the region overlaps a gene in the annotation source.

Requirements

An annotation source to use for annotating the regions.

Output

Three column groups will be created. A summary group, which collapses overlapping annotations to produce a clinically relevant annotation. Second, a full annotation which details the interactions for each transcript-region pair. Finally, a set of columns containing the information in the underlying source.

In the first source we provide the following summary fields:

• Gene Names: The gene which overlaps the variant

• # Genes: Number of genes overlapping this region Transcript Name (Clinically Relevant) The transcript determined to be clinically relevant among those found for the variant’s interaction with the gene.

• Overlapping Exons (Clinically Relevant): Which exons of the transcript overlapping this region, or ‘All’ if they all overlap

• % CDS Covered (Clinically Relevant): The percentage of the exon bases covered by the region.

• % Covered (Clinically Relevant): The percentage of the transcript covered by the region.