University of Michigan Center for Statistical 


GOLD - setup-simwalk2


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.

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-simwalk2 -pped.dat -mmap.dat

An optional parameter (-a) specifies how allele frequencies should be estimated. Possible values are : (-aa) using all individuals in the pedigree; (-af) using all founders in the pedigree; (-ae) assumed to be equal, so that they have no impact on haplotype estimation.



University of Michigan | School of Public Health | Abecasis Lab