5.2 Sample genedrop parameter file

Files for genedrop may be found in the `Simulation' subdirectory of `MORGAN_Examples'. The example here refers to `ped73_gdrop.par'. The seed file can be accessed as through the command line or in the parameter file. If from the parameter file following statements are needed:

input seed file 'marker.seed' output marker seeds only output overwrite seed file 'marker.seed'

The above statements specify `marker.seed' as both the input and output seed file. The statement `output marker seeds only' causes only the marker seeds to be saved before exiting the program. The default is to save both marker and trait seeds. Also, the `overwrite' option in line 4 enables the program to replace the current content in the seed file with the newly generated random numbers, which may be used for simulation in the future. The seed file contains one or more statements like `set marker seeds 0xde5e8d39 0x8ec584dd'. In the example, we have chosen to access the seed file from the command line, hence the first and third lines in the above example are commented out in `ped73_gdrop.par'. See the command line used to simulate data in the next section.

With the statement `output pedigree chronological', the output pedigree will be in chronological order, a requirement for other MORGAN programs to run properly. In addition, a file name must be specified for the output pedigree file. This can be done here in the parameter file using an `output pedigree file' statement or it can be specified on the command line, as shown in the next section.

simulate chrom 1 markers 10 traits 1

The above statement asks genedrop to simulate ten markers loci and one trait locus on chromosome 1. If no trait locus is to be simulated, the part `traits 1' can be removed.

map chrom 1 marker dist 10 10 10 10 10 10 10 10 10

The above statements indicates marker maps on chromosome 1, as specified by map distances (in Haldane centiMorgans). They can also be specified by recombination fractions, e.g. (does not correspond to the above map distances):

map chrom 1 marker recomb fracs 0.1 0.5 0.2

Marker allele frequencies are set by the following lines:

set chrom 1 markers 1 freqs 0.13 0.66 0.16 0.05 set chrom 1 markers 2 freqs 0.06 0.23 0.41 0.25 0.05 set chrom 1 markers 3 freqs 0.11 0.02 0.01 0.06 0.24 0.56 set chrom 1 markers 4 freqs 0.07 0.04 0.89 set chrom 1 markers 5 freqs 0.12 0.11 0.03 0.03 0.50 0.21 set chrom 1 markers 6 freqs 0.50 0.44 0.06 set chrom 1 markers 7 freqs 0.01 0.33 0.62 0.04 set chrom 1 markers 8 freqs 0.20 0.05 0.42 0.27 0.06 set chrom 1 markers 9 freqs 0.18 0.18 0.25 0.16 0.08 0.15 set chrom 1 markers 10 freqs 0.17 0.35 0.04 0.29 0.15

In the case where several markers have the same number of alleles and allele frequencies, one can group those markers together into one line such as

set chrom 1 markers 11 12 13 15 freqs 0.2 0.8

although we consider it good practice to specify the frequencies separately for each marker.

The following five lines describe the trait locus. The trait locus is between markers 2 and 3 on chromosome 5, with recombination fraction 0.1127 to marker 2. The trait locus can have only two alleles; here the frequencies are 0.95 and 0.05, for alleles 1 and 2, respectively. The mean values of the trait for each trait locus genotype are on the next line. Values correspond to the (1 1), (1 2) and (2 2) genotypes, respectively. A non-zero residual variance indicates that there is an environmental component to the trait.

map chrom 1 trait 1 marker 5 dist 5 set trait 1 freqs 0.5 0.5 set trait 1 geno means 90 100 110 set trait 1 residual variance 25.0 set trait 1 additive variance 0.0

The final three lines of the parameter file request that founder gene (or genome) labels and latent variable values for the trait be included in the output file, and data be simulated for all (observed and unobserved) individuals. Founder gene labels indicate, for all non-founders, which founder alleles were passed to the individual. The latent trait variables mentioned in the final statement are the trait locus genotypes and the additive and residual components of the trait value. They will precede the trait value in the output file.

output pedigree record founder gene labels output pedigree record trait latent variables output pedigree record unobserved variables