4.6 Pedigree file

This is a single line entry beginning with code PEDS (can be abbreviated to PED), followed by the name of the pedigree file. There is no default name. This entry is ‘optional’, in such that it is only required if a code of NRM if specified for the covariance structure of a random effect (see 4.9.4). Only one pedigree file can be given. The format of the pedigree file required by WOMBAT is described in detail in 6.3.

By default, WOMBAT fits an animal model. If a sire model is to be fitted, the code SIREMODEL (can be abbreviated to SIR) should be given after the filename.

Additional options, given after the filename and, if applicable the sire model option, that are recognised are +INBR or +SEX. These instruct WOMBAT to read animals’ inbreeding coefficients or sex codes (1=X/2=XX) from the fourth of fifth column in the pedigree file. If given, +INBR causes WOMBAT to skip calculation of inbreeding coefficients and use the values supplied instead. Option +SEX is required if an NRM for X-linked genetic effects is to be set up.