Question: Reference set ExomeDepth

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angele.ctnt •

**10**wrote:Hi everyone,

I'm using ExomeDepth R package for CNV analysis and I have few questions

First, I understand that the reference is chosen by the correlation between each samples, but there is also some column as 'expected.BF', 'phi' ... I don't understand how the tool choose the reference. Is there a threshold ? How can I interpreter the phi value and the expected.BF ?

Also, How is generate the final correlation (<0.97) ? In fact, in my results, the max correlation between each sample is 0.94, however I have a final correlation 0.99

To finish, from how many reads the tools considers that there is a CNV ?

Thank you

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Bouzid.a •

**0**• written 11 months ago by angele.ctnt •**10**
Hi Angele, Did you find clarifications to your questions? I encountered the same ambiguity in my analysis. Thank you,

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