HLAnte: A Python command-line interface for unified HLA genotype annotation with integrated pharmacogenomic, disease,...

The human leukocyte antigen (HLA) system is the most polymorphic gene complex in the human genome and plays a central role in susceptibility to autoimmune disease and drug hypersensitivity. HLA typing tools arcasHLA, T1K, HLA-HD and OptiType each emit a distinct output, creating a manual reformatting bottleneck. We present HLAnte, a Python command-line interface that parses all four formats, normalizes calls against a version-pinned IPD-IMGT/HLA database, and consolidates GWAS Catalog, PharmGKB, Clinical Pharmacogenetics Implementation Consortium (CPIC), and Allele Frequency Net Database (AFND) evidence in one provenance-tagged report. Across 2692 samples from the 1000 Genomes Project, parse rates were 99.8-99.9% and HLAnte matched 26,300 of 26,301 calls to an IPD-IMGT/HLA name; that is coverage, not specificity: only 0.75% of calls resolve to a single allele. We quantified annotation-retrieval fidelity, not clinical detection: CPIC Level 1A retrieval was 100% for four sentinel allele-drug pairs and disease-annotation retrieval 99.7-100% across seven allele-disease pairs. AFND coverage (the proportion of annotated calls with a population allele-frequency record for the sample's super-population) was 99.8-100% in every super-population with the full AFND snapshot. Three worked examples illustrate use: pharmacogenomic triage, population-referenced frequency reporting, and cohort disease-association screening. HLAnte is available under the MIT license (https://github.com/efe3506/HLAnte).