AlphaFamImpute: high accuracy imputation in full-sib families from genotype-by-sequencing data
AlphaFamImpute: high accuracy imputation in full-sib families from genotype-by-sequencing data
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AlphaFamImpute：根据基因型测序数据对全同胞家族进行高精度插补
DOI：
10.1101/2019.12.11.872432
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Whalen A
中科院分区：
文献类型：
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作者：
Whalen A
SummaryAlphaFamImpute是一个用于从单核苷酸多态(SNP)阵列和测序(GBS)数据中调用、分阶段和计算输出的全同胞家系基因组范围的基因类型的计算程序包。GBS数据越来越多地被用于个体的基因分型，特别是当感兴趣的人群不存在SNP阵列时。低覆盖率的GBS产生大量缺失或不正确的幼稚基因呼叫的数据，这可以通过识别全同胞个体之间共享的单倍型片段来改进。在这里，我们介绍了AlphaFamimpute算法，这是一种专门为开发全同胞家庭的遗传结构而设计的算法。它使用两步法来执行补偿。在第一步中，它根据后代的分离状态(即后代继承了哪一对亲本单倍型)来对亲本基因型进行分期和归类。在第二步中，它通过检测后代从父母那里继承了哪些单倍型片段来对后代进行分阶段和归类。通过一系列模拟，我们发现AlphaFamimpute获得了高精度的基因分型，即使父母没有基因分型，个体也在1倍覆盖范围内进行了测序。可用性和实现AlphaFamimpute可以从AlphaGenes网站的http://www.AlphaGenes.roslin.ed.ac.uk/AlphaFamImpute.Supplementary包中获得补充数据可从生物信息学在线获得。
SummaryAlphaFamImpute is an imputation package for calling, phasing and imputing genome-wide genotypes in outbred full-sib families from single nucleotide polymorphism (SNP) array and genotype-by-sequencing (GBS) data. GBS data are increasingly being used to genotype individuals, especially when SNP arrays do not exist for a population of interest. Low-coverage GBS produces data with a large number of missing or incorrect naïve genotype calls, which can be improved by identifying shared haplotype segments between full-sib individuals. Here, we present AlphaFamImpute, an algorithm specifically designed to exploit the genetic structure of full-sib families. It performs imputation using a two-step approach. In the first step, it phases and imputes parental genotypes based on the segregation states of their offspring (i.e. which pair of parental haplotypes the offspring inherited). In the second step, it phases and imputes the offspring genotypes by detecting which haplotype segments the offspring inherited from their parents. With a series of simulations, we find that AlphaFamImpute obtains high-accuracy genotypes, even when the parents are not genotyped and individuals are sequenced at <1x coverage.Availability and implementationAlphaFamImpute is available as a Python package from the AlphaGenes website http://www.AlphaGenes.roslin.ed.ac.uk/AlphaFamImpute.Supplementary informationSupplementary data are available atBioinformaticsonline.