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5.3 Sample genedrop output file

Run the genedrop example using the command:

 
genedrop  genedrop_par  ped good_ped  oped genedrop_oped

If there are more than one `set marker seeds' statements in the seed file (as we append the seeds to this file at the end of the run), the program issues a warning message `Overrides previous statement of same type (W)' for all but the last line to indicate that only the seeds in the last line are used.

The output of genedrop to stdout isn't very interesting but the output pedigree file, required for genedrop, optional for all other MORGAN programs, is. So do take a look at `genedrop.out'.

The output pedigree file has the same structure as the input pedigree file with one individual per record (line). The first four items are the individual's name, the names of the parents and gender. If no addition output options are set, the next items are the genotypes of the markers (two items per marker) in their order on the chromosomes, and the trait values in the order of trait labels.

If `output pedigree record unobserved variables' is given, following gender is the indicator for whether this individual is observed.

If `output pedigree record trait latent variables' is set, three additional items, the genotype, additive and residual components of each trait precede the trait value.

If `output pedigree record founder gene labels' is set, the founder gene labels (two per locus) precede all the marker genotypes.



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