Approximate accuracy program for animal models with genotypes including maternal effect and sire models

ACCF90GS is a modified program of accf90 to calculate reliability for (G)EBV. This is a beta version.

OPTION SNP_file snp

Specify the SNP file name to use genotype data.

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 DiagG_file DiagG

Read a “DiagG” binary file created by preGSf90 with “OPTION saveDiagG”. This option is most stable for many breeds or species.

OPTION DiagGinv_file DiagGimA22i_ren.txt

Read a DiagGimA22i_ren.txt file created by preGSf90. With this beta version, the text file “DiagGimA22i_ren.txt” can be created by preGSf90 using “OPTION saveDiagGimA22iRen” before running accf90GS. This option may not work well in some cases.

OPTION G_file G

Read a G file created by preGSf90. The binary file “G” can be created by preGSf90 using “OPTION saveG” before running accf90GS. This option is required when using the following option: “sum_rel”. This option may not work well in some cases.

OPTION sum_rel avg x.xxx

Calculate the contribution from genotypes using average contribution from genotypes in G with “OPTION rel_PA xx”, where x.xxx is minimum genomic relationship between animals (e.g., 0.0625).

OPTION sum_rel yes x.xxx

Calculate the contribution from genotypes using average reliabilities from genotypes in G with “OPTION rel_PA xx”, where x.xxx is minimum genomic relationship between animals (e.g., 0.0625).

OPTION rel_PA xx

xx = no: multiplied by REL(i), pa: multiplied by REL(PA), or yes: multiplied by REL(j)-REL(PA).

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.