Zmapqtl Options

Table 3.4 shows the command line options specific to Zmapqtl. One can select a trait to analyze, a model for analysis and a walking speed along the genome (that is, the interval between successive analysis points). The user can analyze just one chromosome or the entire genome. Finally, permutation tests or bootstraps can be performed by setting the number of permutations or bootstraps to a number greater than 0. Explanatory variables such as Sex or Line are automatically included in the analysis if their names are preceded by a plus sign in the data file. This is similar to LRmapqtl, except that interaction terms are not yet used.

Table 3.4: Command Line Options for Zmapqtl

Option	Default	Explanation
-i	qtlcart.cro	Input File
-o	qtlcart.z	Output File
-m	qtlcart.map	Genetic Linkage Map File
-l	qtlcart.lr	LRmapqtl Results file
-S	qtlcart.sr	SRmapqtl Results file (Model 6)
-M	3	Model
-t	1	Trait to analyze
-c	0	Chromosome to analyze
-d	2.0	Walking speed in cM
-n	5	Number of Background Parameters (Model 6)
-w	10.0	Window Size in cM (Models 5 and 6)
-r	0	Number of Permutations
-b	0	Number of Bootstraps