SpliceAI or other splice prediction

[gevro]

Hi,
It would be super helpful to add a splice prediction score annotation such as SpliceAI to all variants. Would that be feasible?

Specifically, I'm referring not to annotating with pre-calculated scores, which doesn't encompass all possible variants, but to run the raw score prediction so that every variant has a score prediction.

Thanks

[williamrowell]

Hello,

SpliceAI models are available under a non-commercial license¹, so we won't be able to include SpliceAI annotations. We are evaluating tertiary analysis tools, so if you have any suggestions for splice predictions with less restrictive licenses, we would be interested.

Footnotes

1. https://github.com/Illumina/SpliceAI?tab=License-1-ov-file#readme
   "SpliceAI source code is provided under the GPLv3 license. SpliceAI models are provided under CC BY NC 4.0 license for academic and non-commercial use." ↩

[gevro]

I'll see if I can find another tool. But I'm curious, couldn't your pipeline incorporate spliceAI because you're not charging for use of your open source pipeline, and what matters is whether the end user is commercial? So end users who are not commercial I don't think would go against these terms.

[emmamiz]

Hi,

Could you include Pangolin annotations instead? Their license seems less restrictive:
https://github.com/tkzeng/Pangolin/blob/main/LICENSE

[williamrowell]

Hi @emmamiz, thanks for the suggestion!

I've added Pangolin to an internal task board to evaluate splice annotations for tertiary analysis. We have a lot of internal work on tertiary analysis at the moment that will start making it into versions soon.

Billy

[emmamiz]

Great, thanks Billy!

Also, an open-source version of SpliceAI was recently released— this would be a good addition as well.

https://www.biorxiv.org/content/10.1101/2025.03.20.644351v1

[gevro]

Hi, Any update on this?

[williamrowell]

Sorry, we don't have SpliceAI or Pangolin annotation on the roadmap at this time.