readme.illumina2pregs
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readme.illumina2pregs [2014/05/26 09:56] – ignacio | readme.illumina2pregs [2019/09/27 00:11] – [Optional Arguments] ignacio | ||
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======Summary====== | ======Summary====== | ||
- | Tool for converts | + | Tool for converting '' |
- | Read only AB codes and generates integer variable 0,1,2 or 5 for missing | + | |
+ | Reads 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 '' | ||
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=====Optional Arguments===== | =====Optional Arguments===== | ||
< | < | ||
- | - File name for the map file. Default " | + | 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 | + | Genotype file will be in the same order as given |
- | < | + | < |
- | - Indicate column number for the first allele with code AB (defalut 7) | + | Set GC cutoff (thr) for exclude call (default from GenomeStudio 0.15) |
- | < | + | |
- | | + | |
< | < | ||
- | - Set the maximun length to store alphnumeric | + | Set the maximun length to store alphanumeric |
< | < | ||
- | - Set a file name for output SNP file (default snps2pregs) | + | Set a file name for output SNP file (default snps2pregs) |
=====File formats===== | =====File formats===== | ||
- | Input files | + | ====Input files==== |
- | ----------- | + | '' |
- | SNP_Map.txt: | + | |
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 | ||
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5 index in original SNP_Map.txt | 5 index in original SNP_Map.txt | ||
+ | SNP without defined position (CHR = 0) in the SNP_Map.txt will be located in a new CHR 32 in the output snp_map, but still with 0 position. |
readme.illumina2pregs.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1