By Yutaka Masuda
Renumf90 (version 1.145 or later) supports several methods to assign unknown-parent groups (UPGs) to unknown parents.
You can specify the method by UPG_TYPE, which takes one of the following keywords.
yob: automatic assignment of UPGs based on year-of-birth.in_ped: use of UPG code (negative integer) embedded in pedigreegroup_unisex: manual assignment of UPGs based on user-supplied group code; the same code both for unknown sire and dam.group: as above; separate UPG code for unknown sire and dam.group_sex: as above with flexible UPG assignmentI explain the usage of the last 3 options using the following pedigree file.
A1 0 0 G1 H1 A2 0 0 G1 H2 A3 A2 A1 G2 H1 A4 A3 0 G1 H1 A5 0 A4 G2 H2 A6 A5 A4 G2 H2 A7 A5 A4 G1 H1 A8 0 A7 G1 H1 A9 A8 0 G2 H2
The first 3 columns store the pre-renumbering pedigree (animal, sire, and dam), and the pedigree should have 0 for the unknown parent.
The last 2 columns define groups to which the animal's parents belong.
You need only 1 group code (either column 4 or 5) with group and group_unisex, but two groups with group_sex.
The group code can include any characters.
Renumf90 assumes that the animals with the same group-code have a common UPG.
For example, with the group code in column 4, animal A1 and A8 has the same UPG for sire.
Renumf90 checks the parents of an animal, and if the parent is missing, the program puts a UPG to the missing parents based on the group code of the current animal.
With group_unisex, renumf90 assigns the same UPG code both to unknown sire and dam.
For example, in the above pedigree, A1 will have the same UPG code both for its sire and dam.
With group, you have a separate UPG code for the unknown sire and dam.
For example, A1 will have two different UPG codes for its parents.
Put 6th number on FILE_POS To specify the position of group code in the pedigree file.
For example, use the following description to specify the 4th column for the groups.
FILE_POS 1 2 3 0 0 4
There is a case you need more flexibility.
For example, you may want to assign a separate UPG code to the unknown dam for A1 and A2.
It is not possible to do it using the one-group method (A1 and A2 share the same group code G1 that will assign the same UPG code to their dams).
The keyword group_sex accepts 2 group-columns, and assigns separate UPGs to unknown sire and dam.
If the sire is missing, renumf90 assigns a UPG code based on the 1st group column, and for missing dams, the 2nd group column.
You should put the positions of the group columns in FILE_POS as the 6th and 7th items.
See the following example.
FILE_POS 1 2 3 0 0 4 5
There may be animals that are not in the pedigree file.
For example, some genotyped animals have no pedigree information, and renumf90 puts them as unrelated individuals.
Such additional individuals have missing parents, that should be replaced by UPGs.
Because those individuals are not in pedigree and renumf90 does not know which UPGs are suitable, the program assigns a separate UPG code to their parents by default; the same UPG will be assigned for both parents with group_unisex, and separate UPGs with group and group_sex.
You can define the default UPG for such individuals that do not appear in the pedigree file.
Place DEFAULT_GROUP just after UPG_TYPE in the parameter file, and put the group code.
You need 1 group for group_unisex and group, and 2 groups for group_sex.
# for group UPG_TYPE group DEFAULT_GROUP G1 # for group_sex UPG_TYPE group_sex DEFAULT_GROUP G1 H1