Annotation of DELLY variants

Question

[r00628112]

I ran snpEff for the SV annotation by using this delly results, and found INS/ INV can not be detected by snpeff software. How should I modify the raw input vcf?

[Ram]

Modifying input won't help if a tool is not equipped to handle SVs. You're asking the wrong question - think instead about which tools can help annotate SVs. A quick Google shows a few SV specific tools as well as a VEP blog post about annotating SVs: https://www.ensembl.info/2020/03/27/cool-stuff-the-ensembl-vep-can-do-annotating-structural-variants/