Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add ENFORMER annotations #13

Open
bschilder opened this issue Sep 12, 2022 · 2 comments
Open

Add ENFORMER annotations #13

bschilder opened this issue Sep 12, 2022 · 2 comments
Assignees
Labels
enhancement New feature or request

Comments

@bschilder
Copy link
Member

bschilder commented Sep 12, 2022

Would be great to access all genome-wide ENFORMER predictions via API. This should be possible since the predictions are shared as h5 files here. They're rather massive (14-42Gb each) but that should be mitigated by the h5 database format.

Alternatively, could extract the predictions on-the-fly from the pre-trained model. Usage examples here. But @Al-Murphy has mentioned that the pre-trained model they provide in the paper is not actually the one they describe in the paper.

@bschilder bschilder self-assigned this Sep 12, 2022
@bschilder bschilder added the enhancement New feature or request label Sep 12, 2022
@Al-Murphy
Copy link

Performance of available pre-trained model differs to what they show in the paper but the authors don't seem like they are going to do anything about this so I imagine the model available won't change.

What do you want these predictions for?

@bschilder
Copy link
Member Author

Such a shame, but hopefully the annotations are at least generated by the model described in the paper?

The annotations could be used in at least two scenarios:

  • Computing priors for functional fine-mapping.
  • Conducting enrichment tests to validate fine-mapping SNPs (when not using the same annotations to perform functional fine-mapping).

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
Development

No branches or pull requests

2 participants