AlphaGenome

Topic	Replies	Views	Activity
Updating variant score quantiles Announcements Hi everyone, From the 18th June 2026, we will update our recommended variant scorer quantiles. Previously we computed the score quantiles against a background set of common genetic variants from chromosome 22 (see the “…	0	59	June 11, 2026
Any chance of zebrafish (danRer11) support? Help & Support categorising-content	1	38	June 16, 2026
Reproducing AlphaGenome becnhmarks Help & Support	2	66	June 15, 2026
How to predict TF binding across genome Help & Support	1	49	June 15, 2026
Issue getting new API key Help & Support	2	33	June 12, 2026
Status = StatusCode.INTERNAL error Help & Support	6	66	June 11, 2026
Flagging issue with indel inference and proposed temporary workaround Announcements	1	104	June 8, 2026
What is the correct ontology_curie (UBERON ID) to pull gtex_tissue metadata for GTEx Skeletal Muscle? Help & Support	2	25	June 8, 2026
Reproducing Chrombpnet becnhmarks Help & Support	2	49	June 8, 2026
Validity of raw vs. quantile scores for promoter variant effects when gene body extends beyond 16 kb sequence window Help & Support	1	57	June 2, 2026
Inqiry on Splicing Junction Visualization and Data Extraction Help & Support	1	38	June 2, 2026
Why do only some variants get splicing scores? Help & Support	1	53	June 1, 2026
AlphaGenome Viewer — a web UI for querying AlphaGenome without code Community	1	529	May 24, 2026
RNA-seq effects tend to be higher for variants to the left of the gene Help & Support	2	76	May 21, 2026
HEK293T (EFO:0001184) DNase-seq and CAGE track availability Feedback & Feature Requests	1	26	May 20, 2026
Issues encountered when calling the API Help & Support	1	32	May 20, 2026
New Skill Alert: AlphaGenome Genomic Variant Analysis on Antigravity! Announcements	0	108	May 20, 2026
How can I use the output of histone modifications prediction to interpret the different/significant histone combination in each peak? Help & Support	0	31	May 20, 2026
Variant scorer quantiles not implemented in ag_research Help & Support	4	144	May 15, 2026
REF and ALT tracks look identical even with high quantile_score Help & Support	1	84	May 14, 2026
Ablation Study Clarification: Tiling and Interval Definition for Splice Junctions Help & Support	2	72	May 12, 2026
NN Architecture Feedback & Feature Requests	0	50	May 11, 2026
Best way to aggregate AlphaGenome scores across tracks and modalities for variant prioritization? Help & Support	2	123	May 8, 2026
Can the raw_score values be compared across different cell/sample types, transcription factors, and variants? Help & Support testing	2	83	May 5, 2026
Support for Multi-Base Mutations in AlphaGenome Feedback & Feature Requests	3	1298	April 29, 2026
Clarification on Borzoi tracks used for CAGI5 MPRA benchmarking Help & Support	0	49	April 29, 2026
Can we change the width in the scorer function? Help & Support	4	64	April 29, 2026
ISM implementation/efficiency Help & Support	4	113	April 28, 2026
Sequence centering around non-variant position Help & Support	1	41	April 28, 2026
Interest in building an R wrapper for the AlphaGenome API Community	6	121	April 25, 2026

Updating variant score quantiles

Hi everyone, From the 18th June 2026, we will update our recommended variant scorer quantiles. Previously we computed the score quantiles against a background set of common genetic variants from chromosome 22 (see the “…