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ALT ID CN2, CN3,CN4,CN5 are regions of elevated copy number relative to the reference, Then what does the ID =DUP separately cover? I am new to these analyses. please help

##ALT=<ID=DUP, Description="Region of elevated copy number relative to the reference">
##ALT=<ID=CNO, Description="Copy number allele: 0 copies">
##ALT=<ID=CN2, Description="Copy number allele: 2 copies">
##ALT=<ID=CN3, Description="Copy number allele: 3 copies">
##ALT=<ID=CN4, Description="Copy number allele: 4 copies">
##ALT=<ID=CN5, Description="Copy number allele: 5 copies">
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  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Feb 3, 2023 at 12:41

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The details will depend on the specific tool used to generate the VCF. Each tool has its own system and there is not much standardization for these fields. That said, the likeliest situation here is that if the CNV caller cannot determine the copy number, but only that there is a duplication, it just puts DUP. And if it can determine the specific copy number, then it uses one of the specific terms.

Alternatively, if the copy number is beyond those numbers with a specific CNN value (say you have 7 copies, or 65 or whatever), then it would presumably also use a DUP.

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  • $\begingroup$ Thanks for clarifying @terdon, this output is from Canvas 1.39 $\endgroup$ Feb 3, 2023 at 21:23

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