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

Command-line interface that parses the output of four HLA typing tools, normalises calls against IPD-IMGT/HLA and consolidates GWAS Catalog, PharmGKB, CPIC and AFND evidence in one provenance-tagged report.

The HLA typing tools arcasHLA, T1K, HLA-HD and OptiType each emit a different output format, creating a manual reformatting bottleneck. HLAnte is a Python command-line interface that parses all four formats, normalises calls against a version-pinned IPD-IMGT/HLA database and consolidates GWAS Catalog, PharmGKB, CPIC and AFND evidence in one provenance-tagged report. Across 2692 samples from the 1000 Genomes Project, 99.8-99.9% of outputs were parsed and 26,300 of 26,301 calls matched an IPD-IMGT/HLA name; only 0.75% of calls resolve to a single allele. The authors state they measured annotation-retrieval fidelity, not clinical detection: 100% for four CPIC Level 1A allele-drug pairs. The tool is available under the MIT licence.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

A convenience tool for teams that combine several HLA typers: it removes the reformatting and traces the origin of each annotation. The authors are explicit about the limit: validation covers annotation retrieval, not typing accuracy or clinical benefit; with only 0.75% of calls resolving to a single allele, typing resolution remains the limiting factor. An annotation tool, not a diagnostic test.

Analysis by Dr Thibaut Benquey