6.4 Running markerdrop examples and sample output

The markerdrop examples can be run while in the `Simulation/' subdirectory. The syntax for running a MORGAN program is:

<./program> <parameter file> [> <output file>] or <program> <parameter file> [> <output file>]

if your PATH includes your current directory.

Note that if the output file command is not included, the results will print to the console. To run a simulation of marker data conditional on a trait model, type the following into the console:

./markerdrop ped73_mdrop_trail.par > mdrop_trait.out

Likewise to simulate marker data conditional on an inheritance pattern, type the following:

./markerdrop ped73_mdrop_inhe.par > mdrop_inhe.out

After running markerdrop with the parameter file `mdrop_inhe.par', and the pedigree file `ped73.ped' (as in the above example), the output file `mdrop_inhe.out' is generated. A section of this output file is given below. Note that similar output would be generated using `ped73_mdrop_trait.par'.

Inter-locus distances in cM, using Haldane map function: T3 ----------------------------+------------------------------------------ 10.0 10.0 10.0 1.0 9.0 10.0 10.0 10.0 10.0 10.0 +------+------+------+-------------+------+------+------+------+------+ M1 M2 M3 M4 M5 M6 M7 M8 M9 M10 assigned FGL in all listed individuals: trait locus, followed by 10 marker loci 101 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 102 4 3 4 3 4 3 4 3 4 3 4 3 4 3 4 3 4 3 4 3 4 3 201 2 3 2 3 2 3 2 3 2 3 2 3 2 3 2 3 2 3 2 3 2 3 202 2 4 2 3 2 3 2 3 2 4 2 4 2 4 2 4 2 4 2 4 2 4 2010 6 5 6 5 6 5 6 5 6 5 6 5 6 5 6 5 6 5 6 5 6 5 301 2 6 2 5 2 6 2 6 2 6 2 6 2 5 2 5 2 5 2 5 2 5 302 2 6 3 6 2 6 2 6 2 6 2 5 2 5 2 5 2 6 2 6 2 6 assigned marker genotypes in accordance with data availability: 101 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 102 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 201 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 202 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2010 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 301 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 302 4 2 4 3 5 6 3 3 6 1 1 2 3 3 1 4 1 6 1 4

In the output file above, the marker map is shown, as specified in the parameter file. Below the map, founder genome labels (FGLs) are listed. In this section of the pedigree, individuals 101, 102 and 2020 are founders and so each of them has been assigned two unique FGLs. One of each founder's FGLs has been randomly selected to be passed to their offspring. Using the FGL, marker genotypes have been assigned to individuals on whom data were specified as available in the parameter file, individual 302 for example.