Hi,

I am trying to understand whether a particular CNV called is real or an artifact. The CNV is a DUP with CN = 3. As per my understanding, a good way to examine the coverage change is the variant allele fraction (VAF) for SNVs under the duplication. For regular 2x genome we expect VAF distribution to peak at 0.5 and 1, but 3x duplication, VAF distribution would peak around 0.3, 0.6 and 1. But for this particular CNV, there is a peak at 0.5 and 0.6. I am unsure how to interpret this.