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--- readme.illumina2pregs [2019/09/27 00:11] – [Optional Arguments] ignacio
+++ readme.illumina2pregs [2020/08/25 02:28] – [Optional Arguments] ignacio
@@ Line 34: / Line 34: @@
  Set the maximun length to store alphanumeric IDs (default 10)
 <file>--snpfile_out</file>
- Set a file name for output SNP file (default snps2pregs)
+ 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 snpp_map)
 =====File formats=====
 ====Input files====
 ''SNP_Map.txt''
-Index
- Name
+The following fields should be present in the SNP_Map.txt file,
- Chromosome
- Position
+Any order of columns is supported.
-GenTrain
-Score
+Column positions will be assumed based on the keywords:
-SNP
+  * Name
-ILMN
+  * Chromosome
-Strand
+  * Position
-Customer
+Other fields will be ignored
-Strand
-NormID
+''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
-''FinalReport.txt''
+Optional fields:
+  * GC Score
-SNP_Name
+Other fields will be ignored.
-Sample ID
-Allele1 - Forward
-Allele2 - Forward
-Allele1 - Top
-Allele2 - Top
-Allele2 - AB
-Allele1 - AB
-GC Score
-X
-Y
-** this is the default column position but you can use ''--codeab'' argument for change it the column for
 ====Output files====