CNV analysis

Question

[Cicciongs]

Hello, I have performed Whole-Genome sequencing experiments on two patients blood (human) and one mouse (tail DNA).

Using this data I want to calculate the CNV.

Due to the fact that I do not have any kind of control, I read about several methods related to the general deep coverage of the experiment leading to identifying segments, and so possibly a CNV, without using controls.

I have right now the BAM files obtained using BWA-mem. Can you suggest to me some tools or a general pipeline that will work to identify CNV without controls?

Thank you! Francesco

Answer 1

[Pierre Lindenbaum]

delly2, manta....

Answer 2

[AtenaLia]

You can use CNVkit, in case of WGS can use sample data as a reference for itself. It will work only for very significant (large) changes though.