I am working with 1000 genomes VCF files that I need to annotate with some patients files, I noticed that some variants are annotated as structural variants, with indication
<CN[number-of-CN]>. I was wondering if I can reconvert these variants to INDEL format, e.g.
*22-16050654 A <CN0> [...]*
*22-16050654 A . [...] ?*
*22-16050654 A <CN4> [...] ***-->*** 22-16050654 A AAAAA [...]*
Or it would bring to some conceptual error? Otherwise don't I risk to miss some INDELs? Thanks a lot in advance for any help!