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--- readme.illumina2pregs [2014/05/26 09:58] – [File formats] ignacio
+++ readme.illumina2pregs [2014/05/26 10:07] – [Summary] ignacio
@@ Line 10: / Line 10: @@
 ======Summary======
-Tool for converts FinalReport files from Genome Studio into file suitable for reading with ''pregsf90''
+Tool for converts ''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======
@@ Line 40: / Line 41: @@
 =====File formats=====
-Input files
+====Input files====
------------
+''SNP_Map.txt''
-SNP_Map.txt:
 Index
 Name
@@ Line 56: / Line 56: @@
 NormID
-FinalReport.txt:
+''FinalReport.txt''
-** this is the default but use ''--codeab'' argument for change it
 SNP_Name
 Sample ID
@@ Line 70: / Line 70: @@
 Y
-Output files:
+** this is the default column position but you can use ''--codeab'' argument for change it the column for
--------------
+====Output files====
-snps2pregs:
+''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