6.3 Pedigree File

If the model of analysis contains random effect(s) which are assumed to be distributed proportional to the numerator relationship matrix, a pedigree file is required. It is expected to have the following features:

1. There is no ’default’ name for the pedigree file. File names up to 30 characters long are accommodated.
2. The pedigree file must contain one line for each animal in the data. Additional lines with pedigree information for parents without records themselves can be included.
3. Each line is expected to contain three integer variables :

the animal code,
the code for the animal’s sire,
and the code for the animal’s dam.

All codes must be valid integer in the range of 0  to 2147483647  . Additional, optional variables in the fourth or fifth column can be:

the animal’s inbreeding coefficient (real variable between 0  and 1  ),
a code of 1  (males) or 2  (females) (integer), defining the number of X chromosomes, if a corresponding relationship matrix is to be set up.

4. All animals must have a numerically higher code than either of their parents.
Unknown parents are to be coded as “0”.
5. If maternal genetic effects are to be fitted in the model of analysis, all dams of animals in the data must be ‘known’, i.e. have codes > 0  .
6. The pedigree file does not need to be sorted. However, sorting according to animal code (in ascending order) is desirable, since it will yield slightly reduced processing time.

As for the data file, any lines at the beginning of the pedigree file with a ’#’ (hash sign) in column 1 are ignored.