Varcode, Isovar, and Vaxrank

Library	Responsibility
Varcode	Predict coding consequences and transcript hypotheses from variants.
Isovar	Reconstruct RNA-supported sequences and compare them with those hypotheses.
Vaxrank	Score peptide candidates, select antigen windows and assemble vaccines.

Sequences carry their reference, transcript IDs, frame/completeness and available RNA evidence. Identical proteins retain all contributing sources; different proteins remain separate candidates.

Available today and remaining work

• The ordinary RNA path uses IsovarResult.top_protein_sequence, rather than all entries in sorted_protein_sequences.
• The supplied-fusion adapter retains coding hypotheses and held-out reasons. It runs separately from the small-variant pipeline.
• Opt-in DNA fallback selects a usable changed protein from Varcode outcomes. These candidates have no RNA support.
• Automatic fusion discovery from RNA remains upstream work in Isovar #305.

Other library guides

• Varcode: hypotheses and coding consequences.
• Isovar: RNA reconstruction and reconciliation.