Hi @a7420174 , unfortunately it is difficult for us to diagnose custom VEP configurations, and we don’t use the StructuralVariantOverlap plugin ourselves by default. If you can reproduce this problem on hail dataproc vep with a minimal example (1 line VCF), then we can more likely work through it. You might find this other debugging VEP post useful, and otherwise check the cache directories for any abnormalities. If none of the above is possible, we would suggest running VEP separately. Sorry we could not be more helpful in this instance, we know how frustrating it can be to debug issues when it comes to VEP!