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'. SEED FILE: The seed file is used to store the random seeds used in the simulations. Occasionally one will want to use the same seed with multiple runs, but most often one will want to use new seeds so as to obtain different output with each run. The seed file contains one or more statements like `set marker seeds 0xde5e8d39'. For more about the way genedrop handles seeds See genedrop computational parameters.

The seed file can be specified in the command line or in the parameter file. The following statements are needed to specify the seed file in the parameter file:

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

The first line specifies `marker.seed' as the input seed file for the marker simulation. The default behavior is to save both the marker and trait seeds. The second statement, `output marker seeds only', overrides this default behavior and so causes the program to save only the marker seeds before exiting. The `overwrite' option in line 3 enables the program to replace the current seed file content with the newly generated random numbers, which can be used for simulation in the future. When an overwrite is not requested, MORGAN appends the new output seeds to the existing file at the end of the run. Thus, at the next run, more than one `set marker seeds' statement exists in the seed file. The program uses only the last `set marker seeds' statement in the file.

In the example, we have chosen to access the seed file from the command line, hence the second and third lines in the above example are commented out in `ped73_gdrop.par'. See the next section for command line implementation.

Other notes on the parameter file: The statement `output pedigree chronological' is included in the example `.par' files so that the output pedigree will be in the chronological order required for use with other MORGAN programs.

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 statement indicates a marker map on chromosome 1, with 10 equally spaced markers, each at a distance of 10 (Haldane) centiMorgans from the preceding one.

A marker map can also be specified by recombination fractions. For example:

map chrom 1 marker recomb fracs 0.1 0.5 0.2

gives a map of four ordered markers, M1,M2,M3 and M4, with recombination fraction 0.1 between M1 and M2, 0.5 between M2 and M3, and 0.2 between M3 and M4.

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:

set chrom 1 markers 11 12 13 15 freqs 0.2 0.8

However, 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 5 and 6 on chromosome 1, at a distance of 5 cM to marker 5. The trait locus can have only two alleles; here the frequencies are 0.5 and 0.5, 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. The residual variance gives the within-genotype variance of phenotypic values about the mean. The additive variance (0 in this example, and by default if not specified) is the variance of an additive polygenic contribution to trait values.

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 following three lines may be included in the parameter file (we have commented them out in the example so as to keep the output file small and easy to read).

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

These lines request that the founder gene (or genome) labels and latent variable values for the trait be included in the output file, and that the data be simulated for all (observed and unobserved) individuals. Founder gene labels indicated, for all non-founders, which founder alleles were passed to the individual. The latent and the additive and residual components of the trait value. Latent trait variables will precede the trait value in the output file.