GOLD - setup-eh documentation

Note

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

Input

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

Output

One EH input file for each marker pair. These files will be named as marker_01_and_02.in to marker_NN_and_(NN-1).in, for each marker pair.