Differences

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--- readme.illumina2pregs [2020/08/25 02:28] – [Optional Arguments] ignacio
+++ readme.illumina2pregs [2020/12/09 16:57] – [Output files] 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 36: / Line 36: @@
  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)
+ Set a file name for the output of the MAP file (default snp_map)
 =====File formats=====
@@ Line 79: / Line 79: @@
 ''snp_map''
- index
+ name
 chromosome
 position
- name
+index in original SNP_Map.txt
- 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.