One-way CNV annotation overlap

One-way CNV annotation overlap measures how much of a candidate CNV (previously reported) is covered by the current CNV.

This value is displayed in the Overlap column of the Related cases table and is used by the CNV overlap percentage filter in the Related Cases tab to refine case results based on a user-defined minimum overlap threshold.

How overlap is calculated

1

The number of shared base pairs between the current CNV and a candidate CNV is calculated using their start and end positions:

shared_bp = min(candidate_end, current_end) - max(candidate_start, current_start)

If shared_bp ≤ 0, there is no overlap.

If shared_bp > 0, there is overlap, and the calculation proceeds to the next step.

2

The overlap percentage is calculated as:

overlap% = (shared_bp / candidate_length) × 100

where

candidate_length = candidate_end - candidate_start

Caution:

The calculation is based on coordinates in the same genome build (hg19 or hg38). Both builds are supported, but the two CNVs must be on the same assembly for a correct comparison.

Tips:

• The percentage is asymmetric: it is always relative to the candidate CNV length, not the current CNV. So the same pair can produce different percentages depending on which CNV is treated as “candidate.”

• Both CNVs must be on the same genome build. If they are not, lift-over to a common assembly is required before meaningful overlap calculation.

• If you need a symmetric measure of overlap (for example, “what fraction of either CNV overlaps the other?”), compute both (shared_bp / candidate_length) and (shared_bp / current_length) and examine both percentages.

Examples of one-way CNV annotation overlap

Orange—Current CNV

Violet blue—Previously reported (candidate) CNV

Darker shade—Region of overlap between the current and candidate CNV