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Is the CNQ value the Phred quality score or the confidence percentile?
Dear Genome STRiP users,
I completed the SVCNVDiscovery to all the samples in a single batch. Beside of the CN, I also got the CNQ for the CN of each sample. Based on "https://gatkforums.broadinstitute.org/gatk/discussion/23345/is-there-any-pre-copy-number-value-in-the-processing#latest", CNQ should be the Phred quality score, but my CNQ value looks like
|sample 1||sample 2||sample 3||sample 4||sample 5|
And they look like the confidence percentile, but I am not sure. May I have your help to explain these CNQ values? Thank you very much.