Translocation variants/structural variants input

Help & Support
1

Thanks for sharing the wonderful tool with the genomic research community!

I’m working on structural variants, specifically chromosomal translocations, and I noticed that AlphaGenome uses a feather file for SNP variant input. When dealing with large structural variants, is there a way to use this feather file or the alphagenome/model-internally stored fasta file to specify the sequences we want to stitch together—so the model understands the intended rearrangement—without manually extracting and concatenating sequences from both chromosomes?

Thanks in advance for any guidance!

2

You have to provide the rearranged sequence and use predict_sequence unfortunately. I don’t think you can do variant scoring for variants across chromosomes.

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