The documentation for blupf90 is available separately as a PDF document.
See PREGSF90 with genotypes (SNP) for options.

OPTION conv_crit 1e-12

Set convergence criteria (deault 1e-12).

OPTION maxrounds 10000

Set maximum number of rounds (default 1000).

OPTION solv_method FSPAK

Selection solutions by FSPAK, SOR or PCG (default PCG).

OPTION r_factor 1.6

Set relaxation factor for SOR (default 1.4).

OPTION sol se

Store solutions and standard errors.

OPTION store_pev_pec 6

Store triangular matrices of standard errors and its covariances for correlated random effects such as direct-maternal effects and random-regression effects in “pev_pec_bf90”.

OPTION missing -999

Specify missing observations (default 0).

OPTION residual

y-hat and residual will be included in “yhat_residual”.

OPTION blksize 3

Set block size for preconditioner (default 1).

OPTION prior_solutions

Using the previous solution file to start the iteration. An additional software is required to use this option.

OPTION stdresidual

y-hat and student residuals will be included in “yhat_student_residual”.

OPTION check_levels 0

Check levels (default 1 = true).

OPTION use_yams

Run the program with YAMS (modified FSPAK).

OPTION SNP_file snp

Specify the SNP file name to use genotype data.