I would say this is rather minor, but when running MakeDb.py on IgBlast aa output of TCR delta chains, the predicted locus is always TRA. For IgBlast aa, the only output is the V gene (no J gene), thus the locus is determined based on the V gene only. But all TRD V genes are a subset of the TRA V genes (following the TRAVxx/DVxx pattern).
I'm not sure what the optimal solution for this would be, but I wanted to at least flag the issue so you can decide what to do. You might opt to instead output "TRA/TRD" as locus, though I can foresee that this might cause issues elsewhere. Or perhaps keep the TRA locus, but log a warning if the gene was a shared TRAV/DV gene.
Example IgBlast aa output file with 2 chains annotated as 'delta' by curators:
igblast_delta.txt
I would say this is rather minor, but when running MakeDb.py on IgBlast aa output of TCR delta chains, the predicted locus is always TRA. For IgBlast aa, the only output is the V gene (no J gene), thus the locus is determined based on the V gene only. But all TRD V genes are a subset of the TRA V genes (following the TRAVxx/DVxx pattern).
I'm not sure what the optimal solution for this would be, but I wanted to at least flag the issue so you can decide what to do. You might opt to instead output "TRA/TRD" as locus, though I can foresee that this might cause issues elsewhere. Or perhaps keep the TRA locus, but log a warning if the gene was a shared TRAV/DV gene.
Example IgBlast aa output file with 2 chains annotated as 'delta' by curators:
igblast_delta.txt