PedCheck: A program for identification of genotype incompatibilities in linkage analysis
PedCheck: A program for identification of genotype incompatibilities in linkage analysis
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DOI：
10.1086/301904
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发表时间：
1998-07-01
影响因子：
9.8
通讯作者：
Weeks, DE
中科院分区：
文献类型：
--
作者：
O'Connell, JR;Weeks, DE
在进行连锁分析之前，消除系谱数据中所有孟德尔不一致是必不可少的。通常，通过目视检查鉴定错误的基因型可能非常困难且耗时。事实上，有时错误直到运行链接分析软件的阶段才被识别。然后需要努力找到错误的基因型，并交叉参考可能已经重新编码和重新编号的系谱和标记数据，这不仅是乏味的，而且在非常大的系谱的情况下也是相当令人生畏的。我们已经在一个新的计算机程序PedCheck中实现了四种错误检查算法，该程序将帮助研究人员识别谱系数据中的所有孟德尔不一致性，并为他们提供有用和详细的诊断信息，以帮助解决错误。我们的程序，它使用了许多在VITESSE中实现的算法，快速有效地处理大型数据集，接受各种输入格式，并提供各种错误检查算法，匹配的微妙的系谱错误。这些算法的范围从简单的亲子兼容性检查到基于单位点可能性的统计，该统计识别和排名最有可能出错的个体。我们使用各种真实的数据集来说明我们的计划的权力和有效性。
Prior to performance of linkage analysis, elimination of all Mendelian inconsistencies in the pedigree data is essential. Often, identification of erroneous genotypes by visual inspection can be very difficult and time consuming. In fact, sometimes the errors are not recognized until the stage of running linkage-analysis software. The effort then required to find the erroneous genotypes and to cross-reference pedigree and marker data that may have been recoded and renumbered can be not only tedious but also quite daunting, in the case of very large pedigrees. We have implemented four error-checking algorithms in a new computer program, PedCheck, which will assist researchers in identifying all Mendelian inconsistencies in pedigree data and will provide them with useful and detailed diagnostic information to help resolve the errors. Our program, which uses many of the algorithms implemented in VITESSE, handles large data sets quickly and efficiently, accepts a variety of input formats, and offers various error-checking algorithms that match the subtlety of the pedigree error. These algorithms range from simple parent-offspring-compatibility checks to a single-locus likelihood-based statistic that identifies and ranks the individuals most likely to be in error. We use various real data sets to illustrate the power and effectiveness of our program.