Recombination rates vary significantly across the genome, and estimates of recombination rates are needed for downstream analyses such as haplotype phasing and genotype imputation. Existing methods for recombination rate estimation are limited by insufficient amounts of informative genetic data or by high computational cost. We present a method and software, called IBDrecomb, for using segments of identity by descent to infer recombination rates. IBDrecomb can be applied to sequenced population cohorts to obtain high-resolution, population-specific recombination maps. In simulated admixed data, IBDrecomb obtains higher accuracy than admixture-based estimation of recombination rates. When applied to 2,500 simulated individuals, IBDrecomb obtains similar accuracy to a linkage-disequilibrium (LD)-based method applied to 96 individuals (the largest number for which computation is tractable). Compared to LD-based maps, our IBD-based maps have the advantage of estimating recombination rates in the recent past rather than the distant past. We used IBDrecomb to generate new recombination maps for European Americans and for African Americans from TOPMed sequence data from the Framingham Heart Study (1,626 unrelated individuals) and the Jackson Heart Study (2,046 unrelated individuals), and we compare them to LD-based, admixture-based, and family-based maps.

重组率在整个基因组中有很大差异，下游估计（如单倍型定相和基因型插补）需要重组率的估计。现有的重组率估计方法受到信息基因数据量不足或计算成本高的限制。我们提出了一种方法和软件，称为IBDrecomb，用于通过血统使用同一性片段来推断重组率。IBDrecomb可以应用于已测序的人群队列，以获得高分辨率的，特定人群的重组图。在模拟的混合数据中，IBDrecomb比基于混合的重组率估计获得更高的准确性。当应用于2500个模拟个体时，IBDrecomb获得的准确性与应用于96个个体（计算容易处理的最大数目）的基于连锁不平衡（LD）的方法相似。与基于LD的地图相比，我们基于IBD的地图的优势在于可以估算近期而不是遥远的过去的重组率。我们使用IBDrecomb从Framingham心脏研究（1,626个无关的个体）和Jackson心脏研究（2,046个不相关的个​​体）的TOPM序列数据中为欧洲人和非裔美国人生成了新的重组图谱，并将它们与基于LD的混合物进行了比较以及家庭地图。