CrypticIBDcheck can be used to identify pairs of closely-related subjects based on genetic marker data from single-nucleotide polymorphisms (SNPs). The package is able to accommodate SNPs in linkage disequibrium (LD), without the need to thin the markers so that they are approximately independent in the population. Sample pairs are identified as related by superposing their estimated identity-by-descent (IBD) coefficients on plots of IBD coefficients for pairs of simulated subjects from one of several common close relationships. The methods are particularly relevant to candidategene association studies, in which dependent SNPs cluster in a relatively small number of genes spread throughout the genome.
For more information about the package and its features, please see Nembot-Simo et al. (2013).
The CrypticIBDcheck R package is available on the Comprehensive R Archive Network website under "contributed packages". See the package help file (package?CrypticIBDcheck from within R) for a description of the package features.
You will have to have R installed on your system to use it. To install CrypticIBDcheck you can execute the following command in R:
Windows users can also install the package via the "Packages" menu item.