We envision two different ways to implement variant effect prediction for indels:
A dataloader-based approach that relies on the implementation of a dataloader method that returns full sets of model inputs for the reference and the alternative (+ r.c.) allele of a variant.
A wrapper-based approach similar to how SNVs are handled. Indels will be handled by generating a short reference sequences for the individual alleles, modifying all dataloader input files accordingly. This is envisioned to be performed using g2gtools (there have been efforts recently to enable it for python3)
We envision two different ways to implement variant effect prediction for indels: