Somatic CNV calling in case of pre-existing CNVs

[HenriettaHolze]

Hi, could you explain how reliable CNVkit is for somatic CNV calling in case of "germline" CNVs?
We sequenced a cancer cell line before and after engraftment into mice. I ran CNVkit with the nf-core/sarek pipeline.
When looking at the results for the baseline sample, CNVkit shows a locus with 5 copies at baseline (~2.4M bp).
We are interested in additional CNVs that happened/were selected for during engraftment, i.e. further amplification or loss.
The results of CNVkit and the PURPLE tool (run as part of nf-core/oncoanalyser pipeline) are quite different: CNVkit estimates a somatic CN change of 1.38 (cn=3, log2=0.456329) at the locus. The CN estimated by purple is 2.03.

Below a scatter plot of chr12 for the baseline sample

And for the tumor sample using the baseline as reference

Thanks!