5.3 Running genedrop examples and sample output

Two examples are available under the subdirectory `Simulation/'. The commands to run these examples are similar to the following (see the `README' file in the `Simulation'directory for additional options):

./<program> <parfile> [ped <pedfile>] [seed <seedfile>] [oped <opedfile>] genedrop ped73_gdrop.par ped ../ped73.ped seed ../marker.seed oped gdrop.oped

When running the genedrop example, notice (but do not worry about) the appearance of a warning message on the screen: `Overrides previous statement of same type (W)'. The warning was triggered by the specification of `seeds' as both the input and output seed file, without inclusion of `overwrite' in the `output seed file' statement.Recall from the previous section that, by default, MORGAN appends the new output seeds to the existing seed file at the end of each run. To avoid this warning (and an ever-growing seed file), one can access the seed file from the parameter file and use the `overwrite' option when outputting the seeds (see the previous section Sample genedrop parameter file).

Since the function of genedrop is to simulate marker and trait data, it, unlike other MORGAN programs, always creates and output pedigree file. The output file `gdrop.oped' is structured similarly to the input file `ped73.ped', with one individual per record (line). However, the output file contains additional columns and does not include the parameter statements found at the top of the input file. The first four items are the individual's name, the names of the parents, and gender. If no addition output options are set, the next items are the genotypes of the markers (two items per marker) in the order they are found on the chromosomes, followed by the trait values in the order of the trait labels.

Notice the three statements at the end of the parameter file. In order to save space and make the output more readable, these statements have been commented out so that they are not executed by the program.

If the statement `output pedigree record trait latent variables' was included in the parameter file, the output file would contain four additional columns preceding the trait value. The first two of these columns would be the trait locus genotype, followed by the additive component of the trait value and the residual component of the trait value. In this example, everyone has a `0.000' in the additive component column because we set the additive variance to zero in the parameter file.

If the `output pedigree record founder gene labels' is set, the founder gene labels (FGLs) for markers precede the marker genotypes and the trait FGLs precede the trait locus genotypes (only if latent variables are requested, as in this example).

Also, if the `output pedigree record unobserved variables' statement is included in `gdrop.par', an observed indicator would follow gender in the output pedigree file.