Differences

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--- readme.thrgibbs3 [2016/01/05 21:42] – shogo
+++ readme.thrgibbs3 [2018/04/12 20:31] – [Options] shogo
@@ Line 32: / Line 32: @@
 OPTION solution all
 </file>
+Caution: this option will create a huge output solution file when you run many rounds and/or use a large model.
 Store all samples for solutions in "all_solutions" and posterior means and SD for all effects. The file "all_solutions" could be very large.
 <file>
 OPTION solution all 1 2 3
 </file>
+Caution: this option will create a huge output solution file when you run many rounds and/or use a large model.
 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.
 <file>
@@ Line 68: / Line 70: @@
 OPTION residual 1
 </file>
-Set the residual variance = 1.
+Set the residual variance = 1. For binary traits, the residual variance is automatically set to 1, so no need to use this option.
 <file>
 OPTION pos_def
@@ Line 82: / Line 84: @@
 Specify the SNP file name to use genotype data.
 <file>
-   OPTION hetres_int col nlev
+OPTION hetres_int col nlev
 </file>
 where col is column in the data file that selects which residual (co)variance to select, and nlev is the maximum number of levels. Different residual (co)variances need to be numbered consecutively starting from 1.
@@ Line 120: / Line 122: @@
 </file>
 Give residual covariances for each interval (e.g., x, y, and z).