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--- readme.blupf90 [2018/04/09 23:35] – [Options] shogo
+++ readme.blupf90 [2024/05/15 19:00] (current) – dani
@@ Line 10: / Line 10: @@
 OPTION conv_crit 1e-12
 </file>
-Set convergence criteria (deault 1e-12).
+Set convergence criteria (default 1e-12).
 <file>
 OPTION maxrounds 10000
 </file>
-Set maximum number of rounds (default 1000).
+Set maximum number of rounds (default 5000).
 <file>
 OPTION solv_method FSPAK
@@ Line 34: / Line 34: @@
 OPTION missing -999
 </file>
-Specify missing observations (default 0) in integer.
+Specify missing observations in the data file. Must be an integer value (default is 0).
 <file>
 OPTION residual
@@ Line 42: / Line 42: @@
 OPTION blksize 3
 </file>
-Set block size for preconditioner (default 1).
+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.
 <file>
 OPTION prior_solutions
 </file>
-Using the previous solution file to start the iteration. An additional software is required to use this option.
+The previous solution file will be used to start the iteration. Additional software is required to set up files correctly before using this option.
 <file>
 OPTION stdresidual
@@ Line 64: / Line 64: @@
 Specify the SNP file name to use genotype data.
+<file>
+OPTION snp_p_value
+</file>
+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.
 ==== Omit A-inverse ====