Detection of germinal CNVs with CNVkit

Question

[g.spirito]

Hello, I have a question for CNVkit users.

I aim to detect germline CNVs from blood-derived whole genome sequencing of trios. Occasionally, a CNV that is clearly present in two members of a trio is only called in one of them. That is, the CNV is missing from the .cns or .call.cns file of one member. However, the scatter plot clearly shows the CNV in both members (example in the picture below).

I use the batch command to call CNVs as so:

cnvkit.py batch sample.bam -r reference.cnn -m wgs

I also tried to re-call CNVs with this:

cnvkit.py call sample.cns -o sample_NEW.call.cns --purity 1 -m clonal -v sample.vcf.gz --filter cn --sample-sex f

But the result does not change.

Is there a way I can fine-tune some parameters so that these CNVs are not missed?

Thanks in advance.