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I would use specialized tools for germline. We use a very similar coverage normalization as GATK4 and this comes with a germline workflow. But there are many others.
If you really want to use PureCN, make sure that the normal is not in the pool and do not provide a target weights file (for somatic calling, we try to ignore exons that have a high variance in the PoN). You can try the recommended settings for cell lines (Quick vignette).