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2 hours ago by

Dear everyone,

I had detected CNVs from individual by CNVnator.

So, I have segments and their corresponding normalized RD scores by samples as below.

$cat S1.cnvnator.out

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?

Many thanks.

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