Hello, Thanks for creating such a powerful tool and making it readily available for the research community. I am an oncologist as well as a research scientist. I have been testing AlphaGenome for the past few days and was impressed by its ability to accurately replicate results for single SNP chang…

I have an idea, maybe try it? Since there’s no restriction on variant length, you can try input a variant like this: Chromosome: chr1 (or others) Position: 12345… ref: ACTGCGATTACG (can be longer) alt: ACTACGATTACG This case showed a two-SNP situation, and you can add more as you wish. There …

Hi Jingyu, Thanks for replying. I also thought about this but was not sure if the input sequence would be too long. Good to know that 50kb deletion ran just fine. I will give it a try.

Hi Jingyu, I tried a 7kb sequence with 4 SNPs but it broke AlphaGenome. How was your experience with the large deletion?

Can you show me your error? I’m not sure what happened. In my dataset, there are some large indels. They all work well.

What is your input size? Mine was 7kb. Not sure if that’s too big.

Using AlphaGenome to predict the cooperativity of multiple SNPs?

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Steve_S August 5, 2025, 1:36am 7

never mind, i figured it out

Support for Multi-Base Mutations in AlphaGenome

Topic		Replies	Views
Can AlphaGenome predict the effect of an entire haplotype? Help & Support	1	1031	August 13, 2025
Support for Multi-Base Mutations in AlphaGenome Feedback & Feature Requests	2	1216	September 8, 2025
Multiple Deletions Help & Support	1	169	February 6, 2026
How to properly predict gene expression and histone changes for a large deletion using predict_sequence function Help & Support	3	80	April 2, 2026
Translocation variants/structural variants input Help & Support	1	1379	July 30, 2025

Using AlphaGenome to predict the cooperativity of multiple SNPs?

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