Does the current version of pvacseq run support passing a custom MHC sequence file directly to the underlying NetMHCpan/NetMHCIIpan predictors?
Specifically:
Is there an existing argument in pvacseq run that maps to NetMHCpan's -hlaseq option?
If not, what is the recommended workaround to run the complete pvacseq suite (including downstream filtering and fasta generation) for non-model organisms with custom MHC sequences?
If this is not yet supported, are there any plans to add an option like --mhc-sequence or --hlaseq in future releases?
Does the current version of pvacseq run support passing a custom MHC sequence file directly to the underlying NetMHCpan/NetMHCIIpan predictors?
Specifically:
Is there an existing argument in pvacseq run that maps to NetMHCpan's -hlaseq option?
If not, what is the recommended workaround to run the complete pvacseq suite (including downstream filtering and fasta generation) for non-model organisms with custom MHC sequences?
If this is not yet supported, are there any plans to add an option like --mhc-sequence or --hlaseq in future releases?