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.
