CNV identified by depth but can not be identified by snp allele frequency
CNV identified by depth but can not be identified by snp allele frequency. Depth support that there is one allele of Amplification in chromosome arm. But SNP BAF of that region has no sign as an CNV(enriched at 0.5). My data is sequenced by Illumina(150X, exome, Agilent 50M). Is there any bias of capture system, or this phenomenon is normal?
Thank you for help!
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More details and some example data would be helpful. Exome data is notoriously noisy as a source of CNV estimates. Can you describe in more detail why you believe that there is a single copy amplification of that arm? Did you use a CNV caller? Which one. Also what are the variant allele frequencies there?