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Immunopeptidome builder

Users can build a custom immunopeptidome file based on a selection of HLA alleles. This can be further refined by restricting or excluding Ensembl transcript IDs.

soprano-hla2ip [-h] --alleles HLA_VALUES [HLA_VALUES ...] --output OUTPUT_ID [--cache CACHE_DIR] [--restrict [RESTRICTED_TRANSCRIPT_IDS ...]] [--excluded [EXCLUDED_TRANSCRIPT_IDS ...]]
-h | --help

Get help message

-a | --alleles

1 to 6 space separated HLA alleles, e.g., HLA-A0201 HLA-A0101 HLA-C0701

-o | --output

Name of the output immunopeptidome bed file. No extension required.

-c | --cache

Cache location of the output file. Defaults to app_sources/immunopeptidomes

-r | --restricted

Space separated list of Ensembl transcript IDs to limit immunopeptidome to.

-e | --excluded

Space separated list of Ensembl transcript IDs to exclude from immunopeptidome.