I had detected CNVs from individual by CNVnator.
So, I have segments and their corresponding normalized RD scores by samples as below.
Sample CNV_type coordinates CNV_size normalized_RD
S1 duplication chr1:910101-914800 4700 1.67007
S1 deletion chr1:1288501-1290000 1500 0.127995
S1 deletion chr1:1366701-1367700 1000 0.0266648
S1 deletion chr1:2121701-2124400 2700 0.0418252
S1 deletion chr1:2227301-2229100 1800 0.262821
In several papers, they combined the calls with >80% reciprocally overlapped regions from each individual.
Q1. What is general definition of "reciprocally overlapped region"?
- When all samples share more than 80% reciprocally overlapped region? or
- When two or more samples (any threshold) share more than 80% reciprocally overlapped region?
Q2. How can I merge CNVs from all patients?