Despite its utility, GermlineCNVCaller has some limitations:
Resolution: The resolution of CNV detection depends on the sequencing depth and quality of the data. False Positives/Negatives: Like any bioinformatics tool, there is a risk of false positives or negatives, which can complicate interpretation. Complex CNVs: Detecting complex CNVs, such as those involving multiple breakpoints or regions of low complexity, can be challenging.
