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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DOI：
10.1093/bioinformatics/btaa499
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发表时间：
2020-08-01
期刊：
影响因子：
--
通讯作者：
Hickey JM
中科院分区：
文献类型：
--
作者：
Whalen A;Gorjanc G;Hickey JM
AlphaFamImpute是一个插补软件包，用于从单核苷酸多态性（SNP）阵列和基因型测序（GBS）数据中调用、定相和插补远交全同胞家庭的全基因组基因型。GBS数据越来越多地用于个体基因分型，特别是当SNP阵列不存在于感兴趣的人群中时。低覆盖率GBS产生大量缺失或不正确的幼稚基因型调用的数据，这可以通过识别全同胞个体之间共享的单倍型片段来改善。在这里，我们提出了AlphaFamImpute，专门设计用于利用全同胞家庭的遗传结构的算法。它使用两步方法执行插补。在第一步中，它根据其后代的分离状态（即后代遗传了哪对亲本单倍型）对亲本基因型进行分阶段和估算。在第二步中，通过检测后代从其父母遗传的单倍型片段，对后代基因型进行定相和归责。通过一系列模拟，我们发现AlphaFamImpute获得了高准确度的基因型，即使父母没有进行基因分型，个体的测序覆盖率<1x。AlphaFamImpute可以从AlphaGenes网站http://www.AlphaGenes.roslin.ed.ac.uk/AlphaFamImpute上以Python包的形式获得。 补充数据可在Bioinformatics在线获得。
AlphaFamImpute 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. AlphaFamImpute is available as a Python package from the AlphaGenes website http://www.AlphaGenes.roslin.ed.ac.uk/AlphaFamImpute. Supplementary data are available at Bioinformatics online.
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影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
2.1
作者：
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通讯作者：
Varoquaux, Gael
影响因子：
3.7
作者：
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影响因子：
3.3
作者：
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通讯作者：
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影响因子：
4.1
作者：
Whalen, Andrew;Ros-Freixedes, Roger;Hickey, John M.
通讯作者：
Hickey, John M.