Arguments
founderfile
File containing founder genotypes -
should have 1+(number of founders) columns. The first
column contains the marker names - first space left
blank. The first row for the other columns contains the
founder name. Additional rows contain observed marker
data for all founders.
finalfile
File containing final genotypes - should
have 1+(number of lines) columns. The first column
contains the marker names - first space left blank. The
first row for the other columns contains line names.
Additional rows contain observed marker data for all
lines.
pedfile
File containing pedigree data - should
have three or four columns - first three columns indicate
id, mother and father; fourth column is a flag for
whether the lines was observed.
mapfile
File containing linkage map - should
contain three columns - one for marker names, one for
chromosome assignment and one for map position in cM
phenofile
File containing phenotypic data - should
contain one column for each phenotype, with rows indexing
lines.