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--- undoc:renumf90 [2020/04/21 06:46] – yutaka
+++ undoc:renumf90 [2024/03/25 18:22] (current) – external edit 127.0.0.1
@@ Line 7: / Line 7: @@
 By Yutaka Masuda
-Renumf90 (version 1.145 or later) supports several methods to assign unknown-parent groups (UPGs) to missing parents.
+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.
@@ Line 29: / Line 29: @@
 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 that the animal's parents belong.
+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.
 ===== With one group code =====
@@ Line 39: / Line 40: @@
 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.
+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.
@@ Line 53: / Line 54: @@
 There is a case you need more flexibility.
-For example, you may want to assign a separate UPG code to missing dam for ''A1'' and ''A2''.
+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 one-group method (''A1'' and ''A2'' share the same group code ''G1'' that will assign the same UPG code to their dams).
+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.
@@ Line 63: / Line 64: @@
     FILE_POS
 2 3 0 0 4 5
+===== Default UPG =====
+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