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--- readme.illumina2pregs [2014/06/11 13:45] – [Optional Arguments] dani
+++ readme.illumina2pregs [2019/09/27 00:11] – [Optional Arguments] ignacio
@@ Line 10: / Line 10: @@
 ======Summary======
-Tool for converts ''FinalReport'' and ''SNP_Map.txt'' files from Genome Studio into files suitables for reading with ''pregsf90''
+Tool for converting ''FinalReport'' and ''SNP_Map.txt'' files from Genome Studio into files suitables for reading with ''pregsf90''
 Reads only AB codes and generates integer variable 0,1,2  or 5 for missing
@@ 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 86: / Line 84: @@
 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.