readme.renumf90
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readme.renumf90 [2018/06/05 23:50] – [Options] dani | readme.renumf90 [2022/03/17 18:59] – andres | ||
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=====Fields in the parameter file===== | =====Fields in the parameter file===== | ||
- | # Parameter file for program renf90; it is translated | + | # Parameter file for renumf90. It is translated |
- | # file for BLUPF90 family of programs. | + | |
Lines with # are treated as comments | Lines with # are treated as comments | ||
Line 183: | Line 182: | ||
the default is 3 | the default is 3 | ||
- | all pedigrees are loaded if p=0. | + | all pedigrees are loaded if p=0. To consider all ancestors to be traced back from genotyped and phenotyped animals, put a large number like 100. With p=0, RENUMF90 tries to include all animals found in the raw pedigree file even if the animals in the pedigree are not related to the animals with phenotype or genotype. Thus, p=0 is not recommended. |
< | < | ||
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* if t is ' | * if t is ' | ||
+ | |||
+ | * There are the other values for t: ' | ||
+ | |||
< | < | ||
INBREEDING | INBREEDING | ||
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==== User-defined UPG code ==== | ==== User-defined UPG code ==== | ||
- | The program accepts the following keywords in '' | + | See [[undoc: |
- | | + | The program accepts one of the following keywords in '' |
- | group | + | With one of these options, the program looks at a particular column in the pedigree file as a group code and use it for assigning the UPG code. If an animal has a missing parent, the program assigns a UPG code based on the group code. |
- | + | ||
- | or | + | |
- | + | ||
- | UPG_TYPE | + | |
- | group_unisex | + | |
- | With this option, the program looks at a particular column in the pedigree file as a group code and saves it. If an animal has a missing parent, the program assigns | + | * '' |
+ | * '' | ||
+ | * '' | ||
- | The column in the pedigree file is specified with the 6th item in '' | + | For '' |
FILE_POS | FILE_POS | ||
1 2 3 0 0 5 | 1 2 3 0 0 5 | ||
- | The program now accept 3 items, 5 items, or 6 items in '' | + | For '' |
+ | FILE_POS | ||
+ | 1 2 3 0 0 5 6 | ||
+ | The program now accept 3, 5, 6, or 7 items in '' | ||
=====Extra comments===== | =====Extra comments===== |
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani