BACKGROUND Haplotype data contains more information than genotype data and provides possibilities such as imputing low frequency variants, inferring points of recombination, detecting recurrent mutations, mapping linkage disequilibrium (LD), studying selection signatures, estimating IBD probabilities, etc. In addition, haplotype structure is used to assess genetic diversity and expected accuracy in genomic selection programs. Nevertheless, the quality and efficiency of phasing has rarely been a subject of thorough study but was assessed mainly as a by-product in imputation quality studies. Moreover, phasing studies based on data of a poultry population are non-existent. The aim of this study was to evaluate the phasing quality of FImpute and Beagle, two of the most used phasing software. RESULTS We simulated ten replicated samples of a layer population comprising 888 individuals from a real SNP dataset of 580 k and a pedigree of 12 generations. Chromosomes analyzed were 1, 7 and 20. We measured the percentage of SNPs that were phased equally between true and phased haplotypes (Eqp), proportion of individuals completely correctly phased, number of incorrectly phased SNPs or Breakpoints (Bkp) and the length of inverted haplotype segments. Results were obtained for three different groups of individuals, with no parents or offspring genotyped in the dataset, with only one parent, and with both parents, respectively. The phasing was performed with Beagle (v3.3 and v4.1) and FImpute v2.2 (with and without pedigree). Eqp values ranged from 88 to 100%, with the best results from haplotypes phased with Beagle v4.1 and FImpute with pedigree information and at least one parent genotyped. FImpute haplotypes showed a higher number of Bkp than Beagle. As a consequence, switched haplotype segments were longer for Beagle than for FImpute. CONCLUSION We concluded that for the dataset applied in this study Beagle v4.1 or FImpute with pedigree information and at least one parent genotyped in the data set were the best alternatives for obtaining high quality phased haplotypes.

中文翻译：

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通过基于家庭和人口的软件，对棕色层人口进行阶段性质量评估。

背景技术单倍型数据比基因型数据包含更多的信息，并且提供了诸如估算低频变异，推断重组点，检测复发突变，定位连锁不平衡（LD），研究选择标记，估计IBD概率等可能性。用于评估基因组选择程序中的遗传多样性和预期准确性。尽管如此，定相的质量和效率很少成为深入研究的主题，但在插补质量研究中主要被评估为副产品。而且，不存在基于家禽种群数据的分阶段研究。这项研究的目的是评估最常用的两种调相软件FImpute和Beagle的调相质量。结果我们模拟了十个重复样本，每个样本层包含580个个体，分别来自580 k的真实SNP数据集和12代的谱系。分析的染色体分别是1、7和20。我们测量了真单倍型和分相单倍型（Eqp）之间均等分相的SNP百分比，完全正确分相的个体比例，不正确分相的SNP或断点数（Bkp）以及倒排的长度单倍型片段。获得了三组不同的个体的结果，在数据集中没有父母或后代的基因型，分别只有一个父母和两个父母。分阶段使用Beagle（v3.3和v4.1）和FImpute v2.2（有和没有血统书）执行。Eqp值范围从88％到100％，使用Beagle v4分阶段的单倍型的最佳结果。1，并带有家谱信息和至少一个亲本的基因型进行筛选。快速单倍型显示出比Beagle更高的Bkp数量。结果，比格犬比小猎犬的单倍型节段更长。结论我们得出结论，对于本研究中使用的Beagle v4.1或FImpute带有系谱信息和数据集中至少一个亲本基因型的数据集，是获得高质量分阶段单倍型的最佳选择。