bloodAGENT: a versatile tool for blood group typing and genomic variation analysis.

Motivation: Accurate blood group allele determination is essential for both research and clinical applications. While next-generation sequencing and third-generation sequencing technologies provide a wealth of genomic data, secondary analysis pipelines often struggle with detecting variations in paralogous regions and maintaining haplotype integrity. Existing tools for blood group allele determination are frequently proprietary and lack the flexibility needed to address these challenges. To bridge this gap, we developed bloodAGENT, a versatile and open-source tool designed for analyzing genomic variation and resolving blood group alleles. Results: bloodAGENT achieves high concordance in blood group allele determination under typical conditions but reveals a strong dependence on data completeness. Simulations show that dropout rates are the primary determinant of concordance and ambiguities, with noticeable declines at dropout rates as low as 5%. While phasing breaks have a minor overall impact, their importance remains evident in specific scenarios. These results highlight bloodAGENT's robustness and its potential for handling complex genomic analyses. Availability and implementation: https://github.com/ikmb/bloodAGENT.git.