Delly SCNV calling

[Cactus Z]

Hi group,

I am using delly/1.1.6 to call somatic CNV. I am a bit confused with the output as you can see below.

Why in same region such as mid chr1 no CNV was called. Is it anything to do with the -m mappability map. As I understand that WGS should access the whole genome.

Best

Leilei