How to get actual location of CNV from CNVKit

Question

[rabio]

I know that the CNVkit output is in bins, so I can't get the actual location of the CNV besides the bin. I was wondering if there is a way to get the actual genomic coordinates of a CNV using CNVKit for short read data rather than just finding out the general bin location

Answer 1

[MatthewP]

Hello, use cnvkit.py segment command will give you segments CNV change, which shows the actual genomic coordinates. If you use cnvkit you better read this tutorial.