Some samples may exhibit increased fluctuation in the normalised coverage levels per target region, which is reported in the “result summary” and the per-sample coverage plots in the CNV report. In such cases, it is not possible to distinguish coverage “noise” from real CNVs, and this is why samples may be rejected from CNV calling.
– The fluctuation of the normalized coverage depends on many factors like the purity of the DNA sample, stability of the laboratory conditions and preparation steps, and the number of samples analyzed in a run.
– Analyzing more samples together (of the same gene panel) generally improves the accuracy of the CNV detection and reduces the number of rejected cases.
– The reliability of CNV detection depends much more on the library preparation and amplification steps than on the sequencing step, so high base call quality does not guarantee that CNV calling will be successful.