readme.illumina2pregs
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readme.illumina2pregs [2014/05/26 09:54] – [Usage] ignacio | readme.illumina2pregs [2014/05/26 10:06] – [Summary] ignacio | ||
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======Summary====== | ======Summary====== | ||
- | Tool for converts FinalReport files from Genome Studio into file suitable | + | Tool for converts |
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 '' | ||
- | other options can be modified with optional arguments: | ||
- | Optional Arguments | + | Other options can be modified |
- | * --mapfile | + | |
- | * --genome | + | |
- | * --nosortmap | + | |
- | * --codeab | + | |
- | * --gc <n thr> | + | |
- | * --alphasize | + | |
- | * --snpfile_out | + | |
+ | =====Optional Arguments===== | ||
+ | < | ||
+ | File name for the map file. Default " | ||
+ | < | ||
+ | | ||
+ | < | ||
+ | | ||
+ | < | ||
+ | | ||
+ | < | ||
+ | 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 | + | =====File formats===== |
- | ----------- | + | |
- | SNP_Map.txt: | + | ====Input files==== |
+ | '' | ||
1 Index | 1 Index | ||
2 Name | 2 Name | ||
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12 NormID | 12 NormID | ||
- | FinalReport.txt: | + | '' |
- | ** this is the default but use --codeab for change it | + | |
1 SNP_Name | 1 SNP_Name | ||
2 Sample ID | 2 Sample ID | ||
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11 Y | 11 Y | ||
- | Output files: | + | ** this is the default column position but you can use '' |
- | ------------- | + | ====Output files==== |
- | snps2pregs: | + | '' |
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- | snp_map: | + | '' |
1 index | 1 index | ||
2 chromosome | 2 chromosome |
readme.illumina2pregs.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1