I have a question and hope you guys can help me.
I'm doing a software for a geneticist and she wants to detect deletions and insertions in target exomes in humans. She uses a software where she can see the deepth of coverage in the samples and visually detect if any alteration is present in the exomes of the genes she is interested in.
The problem is that I cannot understand exactly what the name of this problem is. Is it CNV (Copy Number Vatiations) or something else?
Additionaly I asked what sample I should use as control and she said any other sample that used the same experiment could be used as a control sample. The thing is: if I see a difference between the two samples, in which one is the variation? I don't think that makes a lot of sense. Is there a way to get an average .bam file to use as control?
Thank you very much. I really appreciate any help.