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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Gender Inference in Reference Step #821

Open Wonsinsin opened 1 year ago

Wonsinsin commented 1 year ago

Thanks for making such a great tool! I have 40 samples. In these samples, three male samples are always inferred to be female, in the reference step. I check the output of the sex command, and Y_logratio of these three samples is much less than -3, I took a screenshot of the XY ratio related to the three samples. How to deal with this situation？Can I ran reference over all female samples to create a female reference and ran reference ... --male-reference over all male samples to create a male reference? Another way, can I delete these three samples and use the remaining samples to build a normal reference.cnn ? image Thanks for your help.