readme.pcg2
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| readme.pcg2 [2020/07/09 19:54] – [Summary] shogo | readme.pcg2 [2024/03/25 18:22] (current) – external edit 127.0.0.1 | ||
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| Implementation of one-step genomic selection updating animal effects with the combined pedigree and genomic relationship matrix (H-Inverse). | Implementation of one-step genomic selection updating animal effects with the combined pedigree and genomic relationship matrix (H-Inverse). | ||
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| + | //For information on availability of BLUP90IOD, please contact Ignacy Misztal (ignacy@uga.edu) or Daniela Lourenco (danilino@uga.edu) at the University of Georgia.// | ||
| ====== Options ====== | ====== Options ====== | ||
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| OPTION conv_crit 1e-12 | OPTION conv_crit 1e-12 | ||
| </ | </ | ||
| - | Set a convergence criterion (default 1e-12). Usually, a stricter criterion (e.g., 1e-14 to 1e-16) is needed with a single-trait model than a multiple-start model. | + | Set a convergence criterion (default 1e-12). Usually, a stricter criterion (e.g., 1e-14 to 1e-16) is needed with a single-trait model than a multiple-trait model. |
| < | < | ||
| OPTION maxrounds 10000 | OPTION maxrounds 10000 | ||
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| OPTION blksize 3 | OPTION blksize 3 | ||
| </ | </ | ||
| - | Set a block size for preconditioner (default 1) to accelerate convergence (usually 2 to 5 times faster). For a multiple-trait model, | + | Set a block size for preconditioner (default 1) to accelerate convergence (usually 2 to 5 times faster). For a multiple-trait model, |
| < | < | ||
| OPTION init_eq 10 | OPTION init_eq 10 | ||
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| OPTION cont 1 | OPTION cont 1 | ||
| </ | </ | ||
| - | To restart the program from the last solutions. | + | To restart the program from the last solutions |
| < | < | ||
| OPTION missing -999 | OPTION missing -999 | ||
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| OPTION restart 100 | OPTION restart 100 | ||
| </ | </ | ||
| - | Set the number of iteration | + | Set the number of iterations |
| < | < | ||
| OPTION prior_solutions | OPTION prior_solutions | ||
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| OPTION SNP_file snp | OPTION SNP_file snp | ||
| </ | </ | ||
| - | Specify the SNP file name to use genotype data. | + | Specify the SNP file name to use genotype data. \\ |
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| - | //For information on availability of BLUP90IOD, please contact Ignacy Misztal (ignacy@uga.edu) at the University of Georgia.// | + | ==== Storing solutions with original ID ==== |
| + | blup90iod2 allows storing solutions with original ID. To do it, simply add the following option: | ||
| + | OPTION origID | ||
| + | The output is //trait effect level original_id solution//, and is stored in '' | ||
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readme.pcg2.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1