genotype inference

Someone asked about how to use MERLIN to compute IBD. Assuming you're doing inference in three-generation pedigrees, you'll need the flags "--ibd" (to request IBD information), "--singlepoint" (because we're only doing inference where IBD is certain), and "--markerNames" (so that the IBD file will contain marker names instead of locations.)

A typical command to invoke MERLIN should look like

merlin --ibd --singlePoint --markerNames

This is assuming your data is in "merlin.dat", "merlin.map", and "merlin.ped".

For more information, please see

http://genomics.med.upenn.edu/genotypeinference/genotype_inference_software.html