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5.2 Sample genedrop parameter file

Here is the sample parameter file for genedrop, `genedrop_par'.

 
input seed file 'mymarkseeds'
output pedigree chronological
output marker seeds only
output seed file 'mymarkseeds'

The above statements specify `mymarkseeds' as both the input and output seed file. The statement `output marker seeds only' causes only the marker seeds to saved before exiting the program. The default is to save both marker and trait seeds. The seed file contains one or more statements like `set marker seeds 0xde5e8d39 0x8ec584dd'. The output pedigree will be in chronological order, a requirement for other MORGAN programs to run properly.

 
simulate chrom 5 markers 5 traits 1
simulate chrom 7 markers 3

The above two statements ask genedrop to simulate five marker loci and one trait locus on chromosome 5, and another three marker loci (unlinked with the trait) on chromosome 7.

 
map chrom 5 marker dists       25.54 25.54 25.54 25.54
map chrom 7 marker recomb fracs 0.1 0.2 

The above statements indicate marker maps on chromosome 5 and 7, as specified by map distances or recombination fractions.

Marker allele frequencies are set by the following lines:

 
set chrom 5 markers 1 2 3 4 5  freqs 0.2 0.2 0.4 0.2
set chrom 7 markers 1 2 3      freqs 0.2 0.2 0.4 0.2

The remaining four 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, with the rare allele being completely recessive to the common allele. With the (1 1), (1 2) and (2 2) genotypes, we have three genotype means. The residual variance is an environmental component to the trait.

 
map chrom 5 trait 1 marker 2 recomb fract 0.1127
set trait 1 freqs 0.95 0.05
set trait 1 geno means -10.0 0.0 10.0
set trait 1 residual variance 50.0
set trait 1 additive variance 0.0


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