University of Michigan Center for Statistical 


GOLD - setup-eh documentation


Setup-eh is no longer actively supported. To estimate haplotype frequencies using EM, use ldmax.


A linkage format pedigree file (pre-makeped) and a map file listing the markers in pedigree. These are specified by the -p and -m parameters respectively. setup-eh ignores all non-founders in the pedigree, as EH does not handle family data.

For example, to read the pedigree ped.dat, which contains genotypes for the markers listed in map.dat, the following command would be issued:

> setup-eh -pped.dat -mmap.dat


One EH input file for each marker pair. These files will be named as to marker_NN_and_(NN-1).in, for each marker pair.


University of Michigan | School of Public Health | Abecasis Lab