Custom Annotations allow you to annotate custom attributes (labels, scores, and population frequency) to variants or variants within a genomic region.
Select the Configuration icon (gear icon) in the top right area of the screen.
Select the Test Components tab.
Navigate to Custom Annotations.
Select New.
Download the attached template.
Edit the file with the desired annotations. Refer to Custom Annotation File Format.
The supported data categories for custom annotation in Connected Insights are as follows:
Filter: String labels
Score: Numeric values
AlleleFrequency: Allele frequency for population frequency data
Select the Configuration icon (gear icon) in the top right area of the screen.
Select the Test Components tab.
Navigate to Custom Annotations.
Select New.
Upload the file.
On the top toolbar, select Configuration, and then select the Test Components tab.
Select the Custom Annotations section.
Select the desired custom annotation.
Select Download.
After a custom annotation is added to a Test Definition and cases are ingested using the test definition, the variants will be annotated. The annotations can then be viewed and filtered on.
When matching annotations for large variants (structural variants and copy number variants), by default Annotation Overlap (measured as the total overlap divided by the length of the annotation) of >= 0.75 is used, but can be changed to Reciprocal Overlap (measured as the total overlap divided by either the length of the annotation or the length of the variant, whichever is larger) by specifying Reciprocal Overlap in the Description column for the annotation. For more information, refer to Custom Annotation File Format.
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