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--- readme.illumina2pregs [2014/05/26 09:54] – [Usage] ignacio
+++ readme.illumina2pregs [2019/09/27 00:17] – [Input files] ignacio
@@ Line 3: / Line 3: @@
  Ignacio Aguilar - INIA Las Brujas
  email: iaguilar at inia.org.uy
 /10/11 - 06/16/12
 ======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======
-<file> illumina2pregs --snpfile <yourSnpFinalReportFilename> </file>
+<file>illumina2preGS --snpfile <yourSnpFinalReportFilename> </file>
 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>--nosortmap</file>
+ Genotype file will be in the same order as given
+<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 output SNP file (default snps2pregs)
-File formats:
-=============
-Input files
+=====File formats=====
------------
-SNP_Map.txt:
+====Input files====
+''SNP_Map.txt''
 Index
 Name
@@ Line 47: / Line 54: @@
 NormID
-FinalReport.txt:
+''FinalReport.txt''.
-** this is the default but use --codeab for change it
+The following fields should be present in the Final Report file, Any order of columns is supported.
- SNP_Name
+Column positions will be assumed based on the keywords:
- Sample ID
+   SNP_Name
-Allele1 - Forward
+   Sample ID
-Allele2 - Forward
+   Allele2 - AB
-Allele1 - Top
+   Allele1 - AB
-Allele2 - Top
- Allele2 - AB
- Allele1 - AB
-GC Score
-X
-Y
-Output files:
--------------
-snps2pregs:
+Optional fields:
+   GC Score
+====Output files====
+''snps2pregs''
   ID (alphnumeric identification of lenght "alphasize", default 10)
   one space
   genotypes: 0, 1, 2, for AA, AB and BB respectively and 5 for missing.
-snp_map:
+''snp_map''
 index
 chromosome
@@ Line 76: / Line 82: @@
 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.