readme.illumina2pregs
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| readme.illumina2pregs [2014/05/26 09:48] – created ignacio | readme.illumina2pregs [2014/05/26 09:58] – [File formats] ignacio | ||
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| - | =====illumina2pregs===== | + | ====== Illumina2preGS ====== |
| - | - a program to convert genomic information | + | A program to convert genomic information from Illumina files for the BLUPF90 family of programs\\ |
| - | from Illumina files for the BLUPF90 family of programs | + | |
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| ======Summary====== | ======Summary====== | ||
| - | Tool for converts FinalReport files from Genome Studio into file suitable for reading with pregsf90 | + | Tool for converts FinalReport files from Genome Studio into file suitable for reading with '' |
| Read only AB codes and generates integer variable 0,1,2 or 5 for missing | Read only AB codes and generates integer variable 0,1,2 or 5 for missing | ||
| - | ======USAGE====== | + | ======Usage====== |
| - | | + | |
| + | < | ||
| + | |||
| + | The only mandatory argument that is required is the '' | ||
| - | the only mandatory argument that is required is the --snpfile | + | 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 | ||
| Line 47: | Line 57: | ||
| FinalReport.txt: | FinalReport.txt: | ||
| - | ** this is the default but use --codeab for change it | + | ** this is the default but use '' |
| 1 SNP_Name | 1 SNP_Name | ||
| 2 Sample ID | 2 Sample ID | ||
readme.illumina2pregs.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1