5.4.5 genedrop output pedigree options

output pedigree record founder gene labels

When this option is selected, each record contains a pair of founder gene labels for each locus. Each founder is assigned a pair of labels, which are in the same order as the names of the parents. Then, for each locus of 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 included in the output for each trait. The genotype at each trait locus, as well as the additive and residual component of each quantitative trait, will appear in the output record.

output pedigree record unobserved variables

If this option is set, genotypes, gene labels and trait values are output for both observed and unobserved individuals. An additional data field, following the gender indicator, specifies whether the individual is observed (`1') or unobserved(`0').

When this option is not selected, unobserved individuals take on default values; 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 is recorded as `999'.

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 behavior is to indicate in the output pedigree file that the data for these individuals is missing.

assume all observed

When this statement is used, all members of the pedigree are treated as "observed" in the simulation. If an observed indicator column is present in the input file, it is ignored by the simulation.