A high-throughput resequencing technology has brought family based studies back into genetic research focus. Within-family outliers (the individuals whose phenotype is very much unlike the phenotype of relatives) may carry rare variants of large effects and thus resequencing of these provides a highly powered strategy for rare variants detection. On the other hand, such outliers may complicate search for common variants of smaller effects, because they may obscure a real linkage signal. We have developed a program Ped_Outlier allowing automatic detection of within-family outliers in a sample of pedigrees of arbitrary structure and size. We tested our program by identification of within-family outliers for adult height and intracranial volume in large pedigree. Results of linkage analysis of these traits demonstrated that identification of within-family outliers is one of the important steps of pedigree analysis. The program Ped_outlier is freely available at http://mga.bionet.nsc.ru/soft/index.html.
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