OPTIONS

See QTLcart(1) for more information on the global options -h for help, -A for automatic, -V for non-Verbose -W path for a working directory, -R file to specify a resource file, -e to specify the log file, -s to specify a seed for the random number generator and -X stem to specify a filename stem. The options below are specific to this program.

If you use this program without specifying any options, then you will get into a menu that allows you to set them interactively.

-o

This requires a filename for output. Rqtl will overwrite the file if it exists, and create a new file if it does not. If not used, then Rqtl will use qtlcart.qtl.

-i

This requires an input filename. This file must exist. Rqtl will attempt to identify the format of the file and translate it to another format. This file should contain a genetic model defining a set of QTL and including their positions and effects. See the file qtls.inp for the format.

-m

This requires a filename that must exist. Rqtl will read the genetic linkage map from this file.

-t

This allows the user to specify the number of traits to simulate. It is 1 by default.

-q

This requires an integer argument. It allows the user to specify the number of QTL that affect the trait. If one trait is simulated, then exactly this number of QTL will be created. If more than one trait are simulated, then the number of QTL per trait will vary but have mean value specified here. The default is 9.

-d

You can specify the type of dominance at the trait loci. If we assume inbred parental lines with line one marker trait alleles all Q and line two trait alleles all q, then use a 1 for no dominance, a 2 for complete dominance of Q over q, a 3 for complete dominance of q over Q, and a 4 for dominance that is random in direction and magnitude for each locus. It is 1 by default, that is no dominance.

-b

Specifies the parameter needed to determine the additive effect of a QTL. It is 0.5 by default. See Zeng (1992) equation (12) and accompanying text for a discussion of this parameter. Itis not the allelic effect of a QTL allele, rather it is the shape parameter in the beta distribution.

-1, -2

Allows you to specify the two parameters used to determine the dominance effect of a QTL. The effect is simulated from a beta distribution. See the manual for more details.

-E

For a k QTL model, there will be 2k(k+1) potential epistatic terms. This option sets the proportion of epistatic interactions that will be non-zero in a simulated model. The effects are generated with the same beta funtion used for the dominance effects.