6.4 Running markerdrop examples and sample output

To run the two examples under the subdirectory `Simulation/', one may use the following commands:

markerdrop ped73_mdrop_inhe.par

and

markerdrop ped73_mdrop_trait.par

Below is a section of `mdrop_inhe.out', the output file generated using the parameter file `ped73_mdrop_inhe.par' and the pedigree file `ped73_mdrop_inhe.ped'. Similar output would be obtained 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 (FGL) are listed. In this section of the pedigree, individuals 101, 102 and 1020 are founders. They have been assigned two unique FGL each. One of each founder's FGL 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.