自然杀伤 (NK) 细胞是先天免疫系统的重要组成部分，其活性受到杀伤细胞免疫球蛋白样受体 (KIR) 的显着调节。 KIR 基因的多样性和结构复杂性对准确的基因分型提出了重大挑战，这对于了解 NK 细胞功能及其对健康和疾病的影响至关重要。传统的基因分型方法与 KIR 基因的可变性相矛盾，导致不准确，从而阻碍免疫遗传学研究。这些挑战延伸到了最近由人类泛基因组联盟推广的高质量分阶段组装。本文介绍了 BAKIR（KIR 位点的生物信息注释器），这是一种定制的计算工具，旨在克服高质量、定相基因组组装的 KIR 基因分型和注释的挑战。 BAKIR 旨在通过围绕识别关键功能突变构建注释管道来提高 KIR 基因注释的准确性，从而提高基因和等位基因调用的识别和后续相关性。它使用多阶段作图、比对和变体调用过程来确保高精度的基因和等位基因识别，同时还保持相对于已知等位基因数据库显着突变或截短的序列的高召回率。 BAKIR 已在 HPRC 组件的子集上进行了评估，其中 BAKIR 能够改进许多相关注释并调用新变体。 BAKIR 在 GitHub 上免费提供，通过 pip、conda 和奇异容器等多种安装方法提供轻松访问和使用，并配备了用户友好的命令行界面，从而促进了其在科学界的采用。 BAKIR可在 github.com/algo-cancer/bakir 获取。补充数据可在生物信息学在线获取。由牛津大学出版社 2024 年出版。

Natural killer (NK) cells are essential components of the innate immune system, with their activity significantly regulated by Killer cell Immunoglobulin-like Receptors (KIRs). The diversity and structural complexity of KIR genes present significant challenges for accurate genotyping, essential for understanding NK cell functions and their implications in health and disease. Traditional genotyping methods struggle with the variable nature of KIR genes, leading to inaccuracies that can impede immunogenetic research. These challenges extend to high-quality phased assemblies, which have been recently popularized by the Human Pangenome Consortium. This paper introduces BAKIR (Biologically-informed Annotator for KIR locus), a tailored computational tool designed to overcome the challenges of KIR genotyping and annotation on high-quality, phased genome assemblies. BAKIR aims to enhance the accuracy of KIR gene annotations by structuring its annotation pipeline around identifying key functional mutations, thereby improving the identification and subsequent relevance of gene and allele calls. It uses a multi-stage mapping, alignment, and variant calling process to ensure high-precision gene and allele identification, while also maintaining high recall for sequences that are significantly mutated or truncated relative to the known allele database. BAKIR has been evaluated on a subset of the HPRC assemblies, where BAKIR was able to improve many of the associated annotations and call novel variants. BAKIR is freely available on GitHub, offering ease of access and use through multiple installation methods, including pip, conda, and singularity container, and is equipped with a user-friendly command-line interface, thereby promoting its adoption in the scientific community.BAKIR is available at github.com/algo-cancer/bakir.Supplementary data are available at Bioinformatics online.Published by Oxford University Press 2024.