readme.illumina2pregs
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readme.illumina2pregs [2014/05/26 09:52] – ignacio | readme.illumina2pregs [2014/05/26 09:56] – [Illumina2preGS] ignacio | ||
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======Usage====== | ======Usage====== | ||
- | < | ||
- | | + | < |
- | other options can be modified with optional arguments: | + | |
+ | The only mandatory argument that is required is the '' | ||
+ | |||
+ | Other options can be modified with optional arguments: | ||
- | Optional Arguments | + | =====Optional Arguments===== |
- | --mapfile | + | < |
- | --genome | + | - File name for the map file. Default " |
- | --nosortmap | + | < |
- | --codeab | + | - Indicate type of genome (1 - bovine, 2 - ovine) |
- | --gc <n thr> | + | < |
- | --alphasize | + | - Genotype file will be in the same order as given |
- | --snpfile_out | + | < |
+ | - 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: | + | =====File formats===== |
- | ============= | + | |
Input files | Input files |
readme.illumina2pregs.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1