readme.illumina2pregs
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readme.illumina2pregs [2019/09/27 00:11] – [Optional Arguments] ignacio | readme.illumina2pregs [2024/03/25 18:22] (current) – external edit 127.0.0.1 | ||
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< | < | ||
| | ||
- | < | + | < |
- | | + | |
< | < | ||
Set GC cutoff (thr) for exclude call (default from GenomeStudio 0.15) | Set GC cutoff (thr) for exclude call (default from GenomeStudio 0.15) | ||
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Set the maximun length to store alphanumeric IDs (default 10) | Set the maximun length to store alphanumeric IDs (default 10) | ||
< | < | ||
- | Set a file name for output SNP file (default snps2pregs) | + | Set a file name for the output |
+ | < | ||
+ | Set a file name for the output of the MAP file (default snp_map) | ||
=====File formats===== | =====File formats===== | ||
====Input files==== | ====Input files==== | ||
- | '' | + | '' |
- | 1 Index | + | |
- | 2 Name | + | The following fields should be present in the SNP_Map.txt file, |
- | 3 Chromosome | + | |
- | 4 Position | + | Any order of columns is supported. |
- | 5 GenTrain | + | |
- | 6 Score | + | Column positions will be assumed based on the keywords: |
- | 7 SNP | + | * Name |
- | 8 ILMN | + | |
- | 9 Strand | + | |
- | | + | 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: | ||
+ | | ||
+ | * Sample ID | ||
+ | * Allele2 - AB | ||
+ | * Allele1 - AB | ||
- | '' | + | Optional fields: |
+ | * GC Score | ||
- | 1 SNP_Name | + | Other fields will be ignored. |
- | 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 | + | |
- | ** this is the default column position but you can use '' | ||
====Output files==== | ====Output files==== | ||
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'' | '' | ||
- | | + | |
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. | 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