In Ensembl release 110, we have extended the analysis options available for structural variants (SV) in Ensembl VEP including more detailed molecular consequence predictions, more efficient integration of information from reference SV sets, support for breakend variant annotation and the integration of CADD-SV scores.
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Cool stuff the Ensembl VEP can do: annotating structural variants
The Ensembl VEP does not only allow you to annotate short variants, such as SNPs and short insertions or deletions, but also some types of structural variants.