Dose the variantformer support predicting the gene expression caused by the indel?

[Project4bz2023]

Thanks for your excellent job. I have a question: Dose the variantformer support predicting the gene expression caused by the indel? Could you help me? Many thanks.

[sayangsep]

Hi @Project4bz2023 ,
Thanks for your question. Though it wasn't implemented as core functionality, there's a way to do it. You will need to create a VCF file with the variants that you want to test. In this notebooks, we have provided a strategy on how to create a VCF file with all the variants you want to test (check step 2). Additionally, you can add variants to an already existing VCF file to check its influence in the presence of other variants. Please let us know if you have more questions.