I have WGS data sequenced from four normal healthy mouse pituitaries. Two of them were treated with hormone and the other two were untreated. I expected the treated groups would have more CNV events than untreated ones. Which GATK pipeline I should use to call the CNV events? I have went thought all of your somatic/germline CNV analysis tutorials, but fail to find one matching my case. Please advice. Many thanks in advance!
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