ACCF90GS2
Approximate accuracy program for animal models with genotypes including maternal effect and sire models
Summary
ACCF90GS2 is a modified program of accf90 to calculate reliability for (G)EBV based on effective number of records.
Options
OPTION SNP_file snp
Specify the SNP file name to use genotype data.
OPTION readGInverse or readApyGInverse
Read the inverse of the genomic relationship matrix. It must be saved with preGSf90 before using it. The program will not use genomic information without this option.
OPTION diagG
Adjusts genomic reliabilities using the diagonal of G.
OPTION read_external_rel file
Replaces pedigree reliabilities with external reliabilities read from file.
OPTION acc_maxrounds 15
Maximum rounds (default 20). Usually, between 10 and 30.
OPTION conv_crit 1d-06
Convergence criterion (default 1d-06). 1d-05 or 1d-06 to no smaller than 1d-08.
OPTION cg 1 1 2 2
Specify the effect number for contemporary group for each trait. The default is the first effect (= cg 1 1 1 1).
OPTION hs 4
Specify the effect number for herd by sire interaction.
OPTION anim 5
Specify the effect number for animal (required).
OPTION mat 6
Specify the effect number for maternal (required if a maternal effect is included in the model). In a maternal effect model, the next effect of the maternal effect will be automatically the maternal permanent environmental effect (MPE).
OPTION pe 7
Specify the effect number for permanent environment (required if included).
OPTION type 1.0
Select 1.0 for dairy cattle (PTA) or 0.5 for beef cattle (BIF definition) (default 1.0).
OPTION add_residual 8 9
Calculate accuracies adding variances for 8 and 9 random effects to residual variance.
OPTION model animal
Select animal or sire model (default animal).
OPTION parent_avg yes
Output parent averages (default no).
OPTION rel 0.5 0.3
Rescale reliability for traits 1 and 2 if necessary.
OPTION relm 0.5 0.3
Rescale reliability for maternal effect for traits 1 and 2 if necessary.
OPTION disable_mt
Disables multiple-trait adjustment.