readme.illumina2pregs
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readme.illumina2pregs [2014/05/26 09:58] – [File formats] ignacio | readme.illumina2pregs [2019/09/27 00:35] – [Input files] 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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< | < | ||
| | ||
- | < | + | < |
- | | + | 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) | ||
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=====File formats===== | =====File formats===== | ||
- | Input files | + | ====Input files==== |
- | ----------- | + | '' |
- | SNP_Map.txt: | + | The following fields should be present in the SNP_Map.txt |
- | 1 Index | + | Any order of columns is supported. |
- | | + | Column positions will be assumed based on the keywords: |
- | 3 Chromosome | + | |
- | 4 Position | + | |
- | 5 GenTrain | + | |
- | 6 Score | + | Other fields will be ignored |
- | 7 SNP | + | |
- | 8 ILMN | + | |
- | 9 Strand | + | |
- | 10 Customer | + | |
- | 11 Strand | + | |
- | 12 NormID | + | |
- | FinalReport.txt: | ||
- | ** this is the default but use '' | ||
- | 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 files: | + | '' |
- | ------------- | + | 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 | ||
+ | * Allele1 | ||
- | snps2pregs: | + | |
+ | Optional fields: | ||
+ | * GC Score | ||
+ | |||
+ | Other fields will be ignored | ||
+ | |||
+ | ====Output files==== | ||
+ | |||
+ | |||
+ | '' | ||
| | ||
| | ||
| | ||
- | 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