Add AlphaMissense to the annotation sources

Illumina / Nirvana

The nimble & robust variant annotator

https://illumina.github.io/NirvanaDocumentation/

GNU General Public License v3.0

167 stars 44 forks source link

Add AlphaMissense to the annotation sources #114

Open sorgoz opened 10 months ago

sorgoz commented 10 months ago

AlphaFold's team just published a new tool - AlphaMissense: https://www.science.org/doi/10.1126/science.adg7492

Calculated predictions are available at https://zenodo.org/record/8208688 (link taken from the original paper).

It would be great if you guys can add AlphaMissense to the sources for annotation. Thank you!

DarioS commented 8 months ago

It is probably quite similar to PrimateAI-3D, developed by Illumina.

"I am very surprised that AlphaMissense was published in Science after PrimateAI-3D,” says Vasilis Ntranos, senior author of a third recent algorithm, which classified variants based strictly on a protein language model.

Source: AlphaFold-derived AI Predicts Genetic Mutations’ Impact, Chemical & Engineering News

rajatshuvro commented 8 months ago

Hello @sorgoz , @DarioS , thanks you for using Nirvana. Unfortunately, we are not providing AlphaMissense as a natively supported annotation source at this time.

Would you be open to using AlphaMissense via the CustomAnnotation feature provided https://illumina.github.io/IlluminaAnnotatorDocumentation/file-formats/custom-annotations/ ?

Thanks Rajat