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Ask about chromosomal CNVs of a large number of chromosomes
I'm using GATK to call CNVs. It works well for the cases of individual chromosomal CNVs as shown in the tutorial materials. But for the following case, which involves chromosomal CNVs of a large number of chromosomes, I'm wondering if it has overall shifted. I plot the copy ratio and MAF from ACNV procedure, it shows many chromosomes, for example, chromosome 2,4,5,6,7,12,16,17,19,20 (copy ratio close to 1) have MAF around 0.35, while deletion and amplification on other chromosomes are balanced (MAF = 0.5). It makes me a little bit confused, since in most of the cases, if no chromosome CNVs, the MAF should be around 0.5 (balanced); if there are CNVs, the MAF should be other values below 0.5 (unbalanced).
Please correct me if I understand wrong.