Currently, pVACseq does not prefilter transcripts on their biotype. We prioritize protein_coding transcripts when picking the best peptide and transcript in the aggregate report creation.
In pVACsplice we hard-pre-filter on protein_coding transcripts.
Instead we should define a new parameter --biotypes with a default of ['protein_coding'] that applies a prefilter on transcript biotypes both in pVACseq and pVACsplice. The aggregate report will continue to prioritize protein_coding transcripts when selecting the best peptide/transcripts. The docs should explain that "a few other, more speculative types (e.g. non_stop_decay and nonsense_mediated_decay) can give rise to neoantigens if users want to include them, they can specify their own list of biotypes".
Currently, pVACseq does not prefilter transcripts on their biotype. We prioritize protein_coding transcripts when picking the best peptide and transcript in the aggregate report creation.
In pVACsplice we hard-pre-filter on protein_coding transcripts.
Instead we should define a new parameter
--biotypeswith a default of['protein_coding']that applies a prefilter on transcript biotypes both in pVACseq and pVACsplice. The aggregate report will continue to prioritize protein_coding transcripts when selecting the best peptide/transcripts. The docs should explain that "a few other, more speculative types (e.g.non_stop_decayandnonsense_mediated_decay) can give rise to neoantigens if users want to include them, they can specify their own list of biotypes".