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--- readme.illumina2pregs [2018/05/21 15:47] – [Output files] ignacio
+++ readme.illumina2pregs [2019/09/27 00:35] – [Input files] ignacio
@@ Line 29: / Line 29: @@
 <file>--nosortmap</file>
  Genotype file will be in the same order as given
-<file>--codeab  <n></file>
+<file>--gc  <thr></file>
- Indicate column number for the first allele with code AB (defalut 7)
+ Set GC cutoff (thr) for exclude call (default from GenomeStudio 0.15)
-<file>--gc  <n thr></file>
- Set column number (n) of GC and the cutoff (thr) for exclude call (default from GenomeStudio 0.15)
 <file>--alphasize</file>
  Set the maximun length to store alphanumeric IDs (default 10)
@@ Line 42: / Line 40: @@
 ====Input files====
 ''SNP_Map.txt''
-Index
+The following fields should be present in the SNP_Map.txt file,
- Name
+Any order of columns is supported.
- Chromosome
+Column positions will be assumed based on the keywords:
- Position
+  * Name
-GenTrain
+  * Chromosome
-Score
+  * Position
-SNP
+Other fields will be ignored
-ILMN
-Strand
-Customer
-Strand
-NormID
-''FinalReport.txt''
- SNP_Name
+''FinalReport.txt''
- Sample ID
+The following fields should be present in the Final Report file, Any order of columns is supported.
-Allele1 - Forward
+Column positions will be assumed based on the keywords:
- Allele2 - Forward
+  * SNP_Name
- Allele1 - Top
+  * Sample ID
-Allele2 - Top
+  * Allele2 - AB
-Allele2 - AB
+  * Allele1 - AB
-Allele1 - AB
- GC Score
-X
+Optional fields:
-Y
+  * GC Score
+Other fields will be ignored
-** this is the default column position but you can use ''--codeab'' argument for change it the column for
 ====Output files====