Differences

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--- readme.illumina2pregs [2019/09/27 00:35] – [Input files] ignacio
+++ readme.illumina2pregs [2020/12/09 16:56] – [Optional Arguments] ignacio
@@ Line 27: / Line 27: @@
 <file>--genome</file>
  Indicate type of genome (1 - bovine, 2 - ovine)
-<file>--nosortmap</file>
+<file>--sortmap</file>
- Genotype file will be in the same order as given
+ Genotype file will be sorted by chromosome and position
 <file>--gc  <thr></file>
  Set GC cutoff (thr) for exclude call (default from GenomeStudio 0.15)
@@ 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 snp_map)
 =====File formats=====
@@ Line 41: / Line 42: @@
 ====Input files====
 ''SNP_Map.txt''
 The following fields should be present in the SNP_Map.txt file,
 Any order of columns is supported.
 Column positions will be assumed based on the keywords:
   * Name
@@ Line 51: / Line 55: @@
 ''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
@@ Line 62: / Line 68: @@
   * GC Score
-Other fields will be ignored
+Other fields will be ignored.
 ====Output files====