The following is a file prepared partly by Richa Agarwala describing a simple use of SimIBD on a real data set. I have removed references to the data set to avoid revealing any research information. This describes a cookbook usage.
The reference for SimIBD is:
Davis S, Schroeder M, Goldin LR, Weeks DE (1996) Nonparametric simulation-based statistics for detecting linkage in general pedigrees. Am J Hum Genet 58:867-880.
Do not use SimIBD version 1.x.y as it has been superseded by version 2.1 (and possibly later versions).
Required input files:
One output file is produced.
SimIBD currenlty does only 2-point analysis.
SimIBD produces two output files:
This creates simibd.out which summarizes the results of the runs and simibd.aff.out which is the full output from affected comparisons.
The important table is simibd.out with headings: Family ZObs # Aff. Weight Weighted ZObs PValue Range
This will be followed by 1 row of results for each pedigree in your data set.
The Weight column here has to do with the number of affected people in the family, and is unrelated to the allele frequency weight that you were asked to select. For this program you should literally look at the "bottom line" and see if the p-value is small. p-values < 0.05 are considered significant.
SimIBD can be run in parallel. Contact email@example.com for more information.