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readme.illumina2pregs [2014/05/26 09:54] – [Usage] ignacioreadme.illumina2pregs [2020/12/09 16:56] – [Optional Arguments] ignacio
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  Ignacio Aguilar - INIA Las Brujas  Ignacio Aguilar - INIA Las Brujas
 +
  email: iaguilar at inia.org.uy  email: iaguilar at inia.org.uy
 +
  02/10/11 - 06/16/12  02/10/11 - 06/16/12
  
 ======Summary====== ======Summary======
  
-Tool for converts FinalReport files from Genome Studio into file suitable for reading with ''pregsf90'' +Tool for converting ''FinalReport'' and ''SNP_Map.txt'' files from Genome Studio into files suitables for reading with ''pregsf90'' 
-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======
  
-<file> illumina2pregs --snpfile <yourSnpFinalReportFilename> </file>+<file>illumina2preGS --snpfile <yourSnpFinalReportFilename> </file>
  
 The only mandatory argument that is required is the ''--snpfile'' The only mandatory argument that is required is the ''--snpfile''
-   other options can be modified with optional arguments: 
  
-Optional Arguments +Other options can be modified with optional arguments:
-  * --mapfile      - File name for the map file. Default "SNP_Map.txt" +
-  * --genome       - Indicate type of genome (1 - bovine, 2 - ovine) +
-  * --nosortmap    - Genotype file will be in the same order as given  +
-  * --codeab  <n>  - Indicate column number for the first allele with code AB (defalut 7)  +
-  * --gc  <n thr>  - Set column number (n) of GC and the cutoff (thr) for exclude call (default from GenomeStudio 0.15)  +
-  * --alphasize    - Set the maximun length to store alphnumeric IDs (default 10) +
-  * --snpfile_out  - Set a file name for output SNP file (default snps2pregs)+
  
 +=====Optional Arguments=====
 +<file>--mapfile</file>
 + File name for the map file. Default "SNP_Map.txt"
 +<file>--genome</file>
 + Indicate type of genome (1 - bovine, 2 - ovine)
 +<file>--sortmap</file>
 + Genotype file will be sorted by chromosome and position
 +<file>--gc  <thr></file>
 + Set GC cutoff (thr) for exclude call (default from GenomeStudio 0.15) 
 +<file>--alphasize</file>
 + Set the maximun length to store alphanumeric IDs (default 10)
 +<file>--snpfile_out</file>
 + Set a file name for the output of the SNP file (default snps2pregs)
 +<file>--mapfile_out</file>
 + Set a file name for the output of the MAP file (default snp_map)
  
-File formats: +=====File formats=====
-=============+
  
-Input files +====Input files==== 
------------ +''SNP_Map.txt''  
-SNP_Map.txt: +
-   1 Index                                              +
-   2 Name                                               +
-   3 Chromosome                                         +
-   4 Position                                           +
-   5 GenTrain                                           +
-   6 Score                                              +
-   7 SNP                                                +
-   8 ILMN                                               +
-   9 Strand                                             +
-  10 Customer                                           +
-  11 Strand                                             +
-  12 NormID+
  
-FinalReport.txt: +The following fields should be present in the SNP_Map.txt file,   
-** 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 files: +Any order of columns is supported.  
--------------+
  
-snps2pregs:+Column positions will be assumed based on the keywords:                                          
 +  * Name                                               
 +  * Chromosome                                         
 +  * Position                                           
 +Other fields will be ignored 
 + 
 + 
 +''FinalReport.txt''   
 + 
 +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==== 
 + 
 + 
 +''snps2pregs''
    1  ID (alphnumeric identification of lenght "alphasize", default 10)    1  ID (alphnumeric identification of lenght "alphasize", default 10)
    2  one space    2  one space
    3  genotypes: 0, 1, 2, for AA, AB and BB respectively and 5 for missing.    3  genotypes: 0, 1, 2, for AA, AB and BB respectively and 5 for missing.
  
-snp_map:+''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
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