Hi everyone,
I am a PhD student working on GWAS-related research. In this field, we often generate a large number of variant-phenotype associations. However, these variants are mostly located in non-coding regions, which makes it hard to investigate the mechanism of how these variants work.
And Alphagenome jumps out, this tool is very useful for predicting the possible effect of a particular variant. And I started to apply it to my projects. These days, I came up with a very easy window screening method to quickly scan the significant fold changes as a result of variants (from point mutation to indels). I hereby invit everyone to test this method and provide some feedback on this project.
I have uploaded the code to Github: https://github.com/Mirror-fish/AlphaGenome-Variant-Expression-Scanner. The usage and description are provided.
There are still some questions not solved, and Iām still working on it. Anyway, please come try it!
Jingyu