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 (default 1e-12).
OPTION maxrounds 10000
Set maximum number of rounds (default 5000).
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 in the data file. Must be an integer value (default is 0).
OPTION residual
y-hat and residual will be included in “yhat_residual”.
OPTION blksize 3
Set a block size for preconditioner (default 1) to accelerate convergence (usually 2 to 5 times faster). For a multi-trait model, use the number of traits. This option is extremely important to ensure convergence in multi-trait models.
OPTION prior_solutions
The previous solution file will be used to start the iteration. Additional software is required to set up files correctly before using 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.
OPTION snp_p_value
Computes the elements of the inverse of the Mixed Model Equations that are needed for exact GWAS with p-values using postGSf90. This requires quite a lot of memory and time. For details see https://doi.org/10.1101/555243.
OPTION omit_ainv
This option prohibits the program from creating $\mathbf{A}^{-1}$. It is especially useful for GBLUP. For example, if you would like to perform the exact GBLUP, you can put the following options to your parameter file.
OPTION omit_ainv OPTION TauOmega 1.0 0.0 OPTION AlphaBeta 0.95 0.05
With the above options, the program doesn't create $\mathbf{A}^{-1}$ but calculates $\tau\mathbf{G}^{-1}-\omega\mathbf{A}_{22}^{-1}$. When the omega ($\omega$) is zero, only $\mathbf{G}^{-1}$ will be included in the equations. $\mathbf{G}$ is blended with $\mathbf{A}_{22}$ as $\alpha\mathbf{G}+\beta\mathbf{A}_{22}$ before the inversion ($\alpha=0.95$ and $\beta=0.05$ in this case).
Assuming a single-trait ssGBLUP, the mixed model equations are as follows.
\( \left[ \begin{array}{ll} \mathbf{X}'\mathbf{X} & \mathbf{X}'\mathbf{Z}\\ \mathbf{Z}'\mathbf{X} & \mathbf{Z}'\mathbf{Z} + \lambda\mathbf{H}^{-1} \end{array} \right] \left[ \begin{array}{c} \mathbf{\hat{b}}\\ \mathbf{\hat{u}} \end{array} \right] = \left[ \begin{array}{c} \mathbf{X}'\mathbf{y}\\ \mathbf{Z}'\mathbf{y} \end{array} \right] \)
where $\mathbf{H}$ is a matrix combining additive genetic relationship matrices and a genomic relationship matrix.
\( \mathbf{H}^{-1} = \mathbf{A}^{-1} + \left[ \begin{array}{cc} \mathbf{0} & \mathbf{0} \\ \mathbf{0} & \tau\mathbf{G}^{-1}-\omega\mathbf{A}_{22}^{-1} \end{array} \right] \)
If we omit $\mathbf{A}^{-1}$ and $\mathbf{A}_{22}^{-1}$, the equations are equivalent to GBLUP. GBLUP by BLUPF90 was not so easy because the program creates $\mathbf{A}^{-1}$ by default and there was no way to avoid this behavior. The new option removes $\mathbf{A}^{-1}$ from the equations so GBLUP will be easily performed.