readme.illumina2pregs
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readme.illumina2pregs [2014/05/26 09:48] – created ignacio | readme.illumina2pregs [2020/12/09 16:57] – [Output files] 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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+ | |||
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+ | |||
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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 | + | |
- | ======USAGE====== | + | Reads only AB codes and generates integer variable 0,1,2 or 5 for missing |
- | < | + | |
- | the only mandatory argument that is required is the --snpfile | + | ======Usage====== |
- | other options can be modified with optional arguments: | + | |
- | Optional Arguments | + | <file> |
- | --mapfile | + | |
- | | + | |
- | --nosortmap | + | |
- | --codeab | + | |
- | --gc | + | |
- | --alphasize | + | |
- | --snpfile_out | + | |
+ | The only mandatory argument that is required is the '' | ||
- | File formats: | + | Other options can be modified with optional arguments: |
- | ============= | + | |
- | Input files | + | =====Optional Arguments===== |
- | ----------- | + | < |
- | SNP_Map.txt: | + | File name for the map file. Default " |
- | 1 Index | + | < |
- | 2 Name | + | |
- | 3 Chromosome | + | < |
- | 4 Position | + | |
- | 5 GenTrain | + | < |
- | 6 Score | + | Set GC cutoff (thr) for exclude call (default from GenomeStudio 0.15) |
- | | + | < |
- | 8 ILMN | + | Set the maximun length to store alphanumeric IDs (default 10) |
- | 9 Strand | + | < |
- | 10 Customer | + | Set a file name for the output of the SNP file (default snps2pregs) |
- | 11 Strand | + | < |
- | 12 NormID | + | Set a file name for the output of the MAP file (default snp_map) |
- | FinalReport.txt: | + | =====File formats===== |
- | ** this is the default but use --codeab for change it | + | |
- | 1 SNP_Name | + | |
- | 2 Sample ID | + | |
- | 3 Allele1 - Forward | + | |
- | 4 Allele2 - Forward | + | |
- | 5 Allele1 - Top | + | |
- | 6 Allele2 - Top | + | |
- | 7 Allele2 - AB | + | |
- | 8 Allele1 - AB | + | |
- | 9 GC Score | + | |
- | 10 X | + | |
- | 11 Y | + | |
- | Output | + | ====Input |
- | ------------- | + | '' |
- | snps2pregs: | + | The following fields should be present in the SNP_Map.txt file, |
+ | |||
+ | Any order of columns is supported. | ||
+ | |||
+ | Column positions will be assumed based on the keywords: | ||
+ | * Name | ||
+ | * Chromosome | ||
+ | * Position | ||
+ | Other fields will be ignored | ||
+ | |||
+ | |||
+ | '' | ||
+ | |||
+ | The following fields should be present in the Final Report file, Any order of columns is supported. | ||
+ | |||
+ | Column positions will be assumed based on the keywords: | ||
+ | * SNP_Name | ||
+ | * Sample ID | ||
+ | * Allele2 - AB | ||
+ | * Allele1 - AB | ||
+ | |||
+ | |||
+ | Optional fields: | ||
+ | * GC Score | ||
+ | |||
+ | Other fields will be ignored. | ||
+ | |||
+ | ====Output files==== | ||
+ | |||
+ | |||
+ | '' | ||
| | ||
| | ||
| | ||
- | snp_map: | + | '' |
- | | + | |
2 chromosome | 2 chromosome | ||
3 position | 3 position | ||
- | | + | 4 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