readme.illumina2pregs
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| readme.illumina2pregs [2014/05/26 09:52] – ignacio | readme.illumina2pregs [2014/05/26 09:56] – ignacio | ||
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| ======Usage====== | ======Usage====== | ||
| - | < | ||
| - | the only mandatory argument that is required is the --snpfile | + | < |
| - | other options can be modified with optional arguments: | + | |
| - | Optional Arguments | + | The only mandatory argument that is required is the '' |
| - | --mapfile | + | |
| - | --genome | + | |
| - | --nosortmap | + | |
| - | --codeab | + | |
| - | --gc <n thr> | + | |
| - | --alphasize | + | |
| - | --snpfile_out | + | |
| + | Other options can be modified with optional arguments: | ||
| - | File formats: | + | =====Optional Arguments===== |
| - | ============= | + | < |
| + | - File name for the map file. Default " | ||
| + | < | ||
| + | - Indicate type of genome (1 - bovine, 2 - ovine) | ||
| + | < | ||
| + | - Genotype file will be in the same order as given | ||
| + | < | ||
| + | - Indicate column number for the first allele with code AB (defalut 7) | ||
| + | < | ||
| + | - Set column number (n) of GC and the cutoff (thr) for exclude call (default from GenomeStudio 0.15) | ||
| + | < | ||
| + | - Set the maximun length to store alphnumeric IDs (default 10) | ||
| + | < | ||
| + | - Set a file name for output SNP file (default snps2pregs) | ||
| + | |||
| + | |||
| + | =====File formats===== | ||
| Input files | Input files | ||
readme.illumina2pregs.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1