Incorrect Result: CNV Segments Marked as Duplication Despite Copy Ratio Indicating Deletion

[Xscut]

hello

I have encountered an issue with cnvpytor where it incorrectly identifies certain CNV segments as duplications (dup) when the data clearly indicates a deletion. Specifically, in the attached figure, two segments of CNV are highlighted. The copyratio values in the fourth column for these segments range from 0.5 to 0.6, which is indicative of a deletion.

Furthermore, we have confirmed this finding using other detection methods, and they also indicate that these segments are indeed deletions. However, cnvpytor reports them as duplications.

[suvakov]

Thank you for reporting this issue and for providing detailed information. To further investigate and reproduce the bug, it would be helpful if you could share the .pytor file with us. Please send the file to my email: suvakov@gmail.com