Variant scorer quantiles not implemented in ag_research

valeh · March 2, 2026, 7:07pm

Hi,

I am using alphagenome_research to use the model for variant scoring. In the FAQ I see that some variant scorers return a quantiles score. But it looks like this functionality is not implemented in alphagenome_research (only in the alphagenome API):

github.com/google-deepmind/alphagenome

src/alphagenome/models/dna_client.py

2a5318c60


      
          
          var = track_data_utils.metadata_from_proto(
              dna_model_pb2.TracksMetadata(metadata=track_metadata)
          )
          var.index = var.index.map(str)
          
          uns = {'interval': interval}
          if variant is not None:
            uns['variant'] = genome.Variant.from_proto(variant)
          layers = None
          if values.shape[0] > 1:
            layers = {'quantiles': values[1]}
          
          return anndata.AnnData(
              X=values[0],
              obs=obs,
              var=var,
              uns=uns,
              layers=layers,
          )

Is there a reason this is not implement in alphagenome_research?

Thanks.

Tumi_Makgatho · March 4, 2026, 1:55pm

Hi There!

Thanks for reaching out.

Regarding your question about the quantiles score functionality, it is currently only available in the alphagenome API and has not yet been implemented in alphagenome_research.

However, this is on our roadmap, and we are planning to add this feature to alphagenome_research.

Kind regards,
Tumi

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Variant scorer quantiles not implemented in ag_research

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