which pipeline I should use for the CNV calling
Hi,
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!
Joe
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Hi Yizhou Wang,
If your samples are all normal I would suggest using the Germline CNV (gCNV) workflow. Four, however, is very few samples to do analysis with. Do you have more normal mice samples (preferably untreated) that were sequenced with the same technology/protocols etc? If yes, you could use those sample to build a gCNV model using COHORT workflow and then analyze your samples individually with the CASE workflow.
Somatic pipeline could also give some meaningful results but only if you are looking for large events (on order of mega-bases), and again you would ideally need a larger set of normal samples to create a panel of normals.
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