A sample generates >1000 CNV calls, what’s wrong?
Most probably it has low signal quality. Please check the QC&Annotation section in the tutorial to see how to take advantage of the filter_cnv.pl program for automatic QC analysis. It could be also due to heterosomatic CNVs where a fraction of cells lose/gain one chromosomal regions (such as one chromosome arm), so PennCNV gives lots of CNV calls within this region specifically. The 2007 Genome Research paper on PennCNV have some discussions on that, with some illustrations in supplementary figures. In this case, just delete this chromosome in this individual from analysis.
