u/anonutism

Can someone help break down cnv tags for me so I have a more clear idea of how to digest the information? Specifically the tags used in the sequencing.com CNV VCF file.

Included tags:

CN0

CN2

CN3

CN4

CN5

DUP

I presume “CN0 Copy number allele: 0 copies” means that the allele/sequence is deleted on just one chromosome strand, because there is no CN1 tag (which would just be the norm if it’s intended to represent the call on a single strand, whereas if CN0 meant homozygous double strand deletion I would expect CN1 to be a het del and CN2 to be the omitted tag).

However if CN1 is the expected call (and therefore omitted), then what is the difference between CN2 and DUP?