I am using GATK somatic-CNV pipeline for some hg38 human sample (normal-tumor matched). In CollectAllelicCounts interval_list (here and here the discussions) I have tried to use both:

1. gnomad genomes AF>0.02 sites (plot link)

1. sample-specific germline (HaplotypeCaller) called sites (plot link)

I see there are differences but I am not an expert, is anyone able to properly interpret these plots and tell me if the second one has some better resolution than the first one? (as they state in the tutorial: "For allelic count sites, use of sample-specific germline variant sites may incrementally increase resolution.")

Thank you very much in advance for any help!