JZmapqtl Options

Table 3.6 shows the command line options specific to JZmapqtl. Most are the same as those for Zmapqtl. One thing to note is that there is no facility for permuation tests or bootstraps at this time.

Table 3.6: Command Line Options for JZmapqtl

Option	Default	Explanation
-i	qtlcart.cro	Input File
-o	qtlcart.z	Output File
-e	qtlcart.log	Error File
-m	qtlcart.map	Genetic Linkage Map File
-S	qtlcart.sr	SRmapqtl results (Model 6)
-E	qtlcart.eqt	Eqtl results (Model 7)
-s	893339277	Random Number Seed
-M	3	Model [3,6,7], 3$=>$IM
-t	1	Trait to analyze
-c	0	Chromosome to analyze (0$=>$all)
-d	2.000000	Walking speed in cM
-n	5	Highest rank for Background Parameters (Model 6)
-w	10.000000	Window Size in cM (Model 6)
-I	1	Hypothesis test