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.