Detection of CNVs
After calculating each exon coverage using Depth of Coverage module in GATK, how to normalize each exon depth and calculate copy number ratio?
There are multiple possible solutions. I would suggest having a look at published algorithms, and a good place to start would be https://omictools.com/cnv-detection2-category
More precisely, XHMM starts from coverage depth calculated by GATK. But there are multiple other tools (exomeCopy, codex, conifer,...)
The key point of CNV detection is you have to make a baseline from controls, and do the normalization based on the baseline.
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