The GIBBS3F90 version with heterogenous residual variances for THRGIBBS1F90.

The parameter file is the same as for THRGIBBS1F90 except for heterogeneity.

OPTION cat 0 0 2 5

“0” indicate that the first and second traits are linear. “2” and “5” indicate that the third and fourth traits are categorical with 2 (binary) and 5 categories.

OPTION fixed_var all

Store all samples for solutions in “all_solutions” and posterior means and SD for all effects in “final_solutions”, assuming that (co)variances in the parameter file are known.

OPTION fixed_var all 1 2 3

Store all samples for solutions in “all_solutions” and posterior means and SD for 1, 2, and 3 effects in “final_solutions”.

OPTION fixed_var mean

Only posterior means and SD for solutions are calculated for all effects in “final_solutions”.

OPTION fixed_var mean 1 2 3
Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in "final_solutions".

OPTION solution all

Store all samples for solutions in “all_solutions” and posterior means and SD for all effects. The file “all_solutions” could be very large.

OPTION solution all 1 2 3

Store all samples for solutions in “all_solutions” and posterior means and SD for 1, 2, and 3 effects. The file “all_solutions” could be very large.

OPTION solution mean

Only posterior means and SD for solutions are calculated for all effects in “final_solutions”.

OPTION solution mean 1 2 3

Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in “final_solutions”.

OPTION cont 10000

“10000” is the number of samples run previously. The user can restart the program from the last run.

OPTION prior 5 2 -1 5 

The (co)variance priors are specified in the parameter file.
Degree of belief for all random effects should be specified using the following structure:
OPTION prior eff1 db1 eff2 db2 … effn dbn -1 dbres
effx correspond to the effect number and dbx to the degree of belief for this random effect, -1 corresponds to the degree of belief of the residual variance.
In this example 2 is the degree of belief for the 5th effect, and 5 is the degree of belief for the residual.

OPTION seed 123 -432

Two seeds for a random number generator can be specified.

OPTION thresholds 0.0 1.0 2.0

Set the fixed thresholds. No need to set 0 for binary traits.

OPTION residual 1

Set the residual variance = 1.

OPTION pos_def

Specify checking pos-def for fixed effects.

OPTION censored 1 0

Negative values for the categorical trait in the data set indicate censored records. “1 0” determines that the first categorical trait is censored and the second uncensored.

OPTION SNP_file snp

Specify the SNP file name to use genotype data.