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genedrop
output pedigree options
output pedigree record founder gene labels
When this option is selected, each record contains, for each locus, a pair of founder gene labels. Each founder is assigned a pair of labels, which are in the same order as the names of the parents. Then, for each locus for each descendant, founder labels are determined by the simulated meiosis indicators.
This statement is useful in cases where we want the "disease" allele in the pedigree to come from a particular founder.
output pedigree record trait latent variables
This statement requests that the quantitative trait value be output for each trait. With this option, additional items appear in the record: the genotype at each trait locus and the additive and residual component of each quantitative trait.
output pedigree record unobserved variables
When this option is not selected, unobserved individuals have the genotype at each locus represented as `0 0', the founder gene label (if requested) at each locus represented as `0 0', and each quantitative trait value given as `999'.
If this option is set, then genotypes, gene labels and trait values are output for unobserved individuals, as well as for the observed members of the pedigree. An additional data field, following the gender indicator, specifies whether or not the individual is observed. `0' indicates unobserved, `1', observed.
input pedigree record observed (absent | present)
The observed indicator is used to designate which members are observed, with '0' indicating unobserved, '1' indicating observed. When the observed indicator is present in the pedigree file, it follows gender (or parents, if gender is not present). If this statement is not given, all pedigree members are assumed to be observed. See also the next statement `assume all observed'.
If individuals are flagged, in the pedigree file, as unobserved, the default is to indicate, in the output pedigree file, the data for these individuals as missing.
assume all observed
This statement results in all members of the pedigree "observed" in the simulation, with the observed indicator, if present in the input file, ignored.
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