StructuralVariantOverlap: extremely slow

[fgvieira]

Dear all,

I am running StructuralVariantOverlap on ~16000 SVs and it takes more than one day! I've been having this issue for a while and I've opened an issue on VEP, but not sure where the best way to fix it.

Is there any other way to speed it up?

thanks,

[dglemos]

Hi @fgvieira,
thanks for reporting this issue, we run a few tests and we can replicate the issue.
The plugin checks every variant individually which increases the running time. We don't have a fix right now but we are looking into a way to improve its performance.
About the vep issue #743, I have to talk with the team to see if we can restrict the annotations to a subset but if you have issues with the standard vep running time you could send a few examples and we'll look into it.