Command Line Options

Table 2.1 summarizes the command line options for Rmap. Most of these were explained in 2.1.1. The default options in Table 2.1 would produce a genetic linkage map on four chromosomes with 16 markers each. The markers would be equally spaced at 10 centimorgan intervals and would span the genome.

Table 2.1: Command Line Options for Rmap

Option	Default	Explanation
-i		Input File
-o	qtlcart.map	Output File
-f	1	Map Function
-p	0.0	Map function parameter
-g	1	Output Flag
-c	4	Chromosomes
-m	16	Markers per Chromosome
-vm	0.0	Standard deviation of Markers per Chromosome
-d	10.0	Intermarker Distance (cM)
-vd	0.0	Standard deviation of Intermarker Distance
-t	0.0	Tails (Flanking DNA, in cM)
-M	0	Simulation Mode (0,1)