Closed pnrobinson closed 10 months ago
Look into variant_effects
list and check if we have a splice effect. If yes, then we do not log a warning regarding missing protein coordinates.
We don't mind missing the protein coordinates for these effects:
SPLICE_DONOR_VARIANT
SPLICE_DONOR_5TH_BASE_VARIANT
SPLICE_ACCEPTOR_VARIANT
SPLICE_POLYPYRIMIDINE_TRACT_VARIANT
This is expected. I think we need to slightly refactor the way the analysis starts. We need to give the analysis a reference transcript (not a reference protein). It also does not make sense to test multiple proteins (or transcripts) at once. For any conceivable clinical analysis, people focus on one transcript, which in almost all cases is (or should be) the MANE or ClinVar transcript. Having this much choice will engender confusion and not bring benefits!