What are the approaches folks are using for IBD calculation in whole genome data from extended families (4-generations)? Has anyone tried using the typical linkage-like software like merlin or genehunter?
Thanks, Zev, for the answer below. This is a good resource, but solves a slightly different problem than what I had in mind. We have the pedigree structure and the genotype data and want to infer the IBD states of all individuals in the pedigree (so that we can perform non-parametric linkage analysis, basically).
We like the ERSA tool from the Jorde lab:
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