Inferring Coancestry in Population Samples in the Presence of Linkage Disequilibrium

http://www.stat.washington.edu/thompson/Genepi/pangaea.shtml

1. The IBD_Haplo software (which consists primarily of the ibd_haplo program) runs as a part of our MORGAN-3 package. The analyses of this article were run with the version of ibd_haplo in MORGAN 3.0.3 (November 2011 release).
2. A small collection of programs has been released (October 2011) under the name Create_IBD. This includes the beaglesim procedure (both as R-code and as a C-program) and programs for the population ibd simulation, and for the assignment of haplotypes to descendant chromosome segments.
3. The R-package, IBDhaploRtools, is used in analysis of ibd_haplo output. Version 1.2 (November 2011 release) performs the result summaries included in this article. The R-package also contains a tutorial, generated from an Sweave document, enabling the user to replicate the steps of analysis used to produced the tables and figures of this article fromibd_haplo output files.
4. Data files from this study are provided as supporting information in the form of two compressed file archives; see Supporting Information, File S1 for details. The first archive (see File S2) includes the simulation truth of the ibdamong the 500 pairs of individuals used in this study and the marker information and data haplotypes of the relevant individuals generated at four different LD levels (γ = 0.0, 0.05, 0.1, 1.0). The second archive (see File S3) contains interim output of our analyses in the form of Rdata files of inferredibd states, together with an Sweave wrapper document that uses these files in conjunction with the IBDhaploRtools R-package to recreate the tables and figures of this article. In principle, the results of File S3 and of this article can be recreated from only the data in File S2, using the ibd_haplo program, but this involves many huge intervening input and output files.