Hi there,
Thank you for reaching out.
Currently, score_variant is designed for single variants. You can try creating a single structured variant with all the deletions by defining the reference_bases as the entire genomic span covering the sites and the alternate_bases as that sequence with the fragments removed. Alternatively, manually construct the full DNA sequence string with all 6 fragments removed and input this custom sequence into the predict_sequence() function,. You will then need to manually compare these predictions to those from the reference sequence to determine the combined effect.
Please also refer here for further assistance Using AlphaGenome to predict the cooperativity of multiple SNPs?
Kind regards,
Tumi