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| readme.illumina2pregs [2014/05/26 09:52] – ignacio | readme.illumina2pregs [2014/05/26 09:54] – [Usage] ignacio |
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| ======Usage====== | ======Usage====== |
| <file> illumina2pregs --snpfile <yourSnpFinalReportFilename> <\file> | |
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| the only mandatory argument that is required is the --snpfile | <file> illumina2pregs --snpfile <yourSnpFinalReportFilename> </file> |
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| | The only mandatory argument that is required is the ''--snpfile'' |
| other options can be modified with optional arguments: | other options can be modified with optional arguments: |
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| Optional Arguments | Optional Arguments |
| --mapfile - File name for the map file. Default "SNP_Map.txt" | * --mapfile - File name for the map file. Default "SNP_Map.txt" |
| --genome - Indicate type of genome (1 - bovine, 2 - ovine) | * --genome - Indicate type of genome (1 - bovine, 2 - ovine) |
| --nosortmap - Genotype file will be in the same order as given | * --nosortmap - Genotype file will be in the same order as given |
| --codeab <n> - Indicate column number for the first allele with code AB (defalut 7) | * --codeab <n> - Indicate column number for the first allele with code AB (defalut 7) |
| --gc <n thr> - Set column number (n) of GC and the cutoff (thr) for exclude call (default from GenomeStudio 0.15) | * --gc <n thr> - Set column number (n) of GC and the cutoff (thr) for exclude call (default from GenomeStudio 0.15) |
| --alphasize - Set the maximun length to store alphnumeric IDs (default 10) | * --alphasize - Set the maximun length to store alphnumeric IDs (default 10) |
| --snpfile_out - Set a file name for output SNP file (default snps2pregs) | * --snpfile_out - Set a file name for output SNP file (default snps2pregs) |
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