Segments of identity by descent (IBD) are used in many genetic analyses. We present a method for detecting identical-by-descent haplotype segments in phased genotype data. Our method, called hap-IBD, combines a compressed representation of haplotype data, the positional Burrows-Wheeler transform, and multi-threaded execution to produce very fast analysis times. An attractive feature of hap-IBD is its simplicity: the input parameters clearly and precisely define the IBD segments that are reported, so that program correctness can be confirmed by users. We evaluate hap-IBD and four state-of-the-art IBD segment detection methods (GERMLINE, iLASH, RaPID, and TRUFFLE) using UK Biobank chromosome 20 data and simulated sequence data. We show that hap-IBD detects IBD segments faster and more accurately than competing methods, and that hap-IBD is the only method that can rapidly and accurately detect short 2-4 centiMorgan (cM) IBD segments in the full UK Biobank data. Analysis of 485,346 UK Biobank samples through the use of hap-IBD with 12 computational threads detects 231.5 billion autosomal IBD segments with length ≥2 cM in 24.4 h.

中文翻译：

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一种快速、简单的方法，用于检测大规模数据中的逐个血统片段。

血统同一性片段 (IBD) 用于许多遗传分析。我们提出了一种检测阶段性基因型数据中血统相同的单倍型片段的方法。我们的方法称为 hap-IBD，结合了单倍型数据的压缩表示、位置 Burrows-Wheeler 变换和多线程执行，以产生非常快的分析时间。hap-IBD 的一个吸引人的特点是它的简单性：输入参数清楚、精确地定义了报告的 IBD 段，以便用户可以确认程序的正确性。我们使用英国生物银行 20 号染色体数据和模拟序列数据评估 hap-IBD 和四种最先进的 IBD 片段检测方法（GERMLINE、iLASH、RaPID 和 TRUFFLE）。我们表明，hap-IBD 比竞争方法更快、更准确地检测 IBD 片段，并且 hap-IBD 是唯一能够在完整的英国生物库数据中快速、准确地检测短 2-4 厘摩 (cM) IBD 片段的方法。通过使用具有 12 个计算线程的 hap-IBD 对 485,346 个英国生物银行样本进行分析，在 24.4 小时内检测到 2315 亿个长度≥2 cM 的常染色体 IBD 片段。