User Tools

Site Tools


readme.illumina2pregs

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
readme.illumina2pregs [2019/09/27 00:36]
ignacio [Input files]
readme.illumina2pregs [2020/12/09 16:57] (current)
ignacio [Output files]
Line 27: Line 27:
 <​file>​--genome</​file>​ <​file>​--genome</​file>​
  ​Indicate type of genome (1 - bovine, 2 - ovine)  ​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>​ <​file>​--gc ​ <​thr></​file>​
  Set GC cutoff (thr) for exclude call (default from GenomeStudio 0.15)   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)  Set the maximun length to store alphanumeric IDs (default 10)
 <​file>​--snpfile_out</​file>​ <​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===== =====File formats=====
Line 78: Line 79:
  
 ''​snp_map''​ ''​snp_map''​
-   ​1 ​index+   ​1 ​name 
    2 chromosome    2 chromosome
    3 position ​    3 position ​
-   ​4 ​name  +   4 index in original SNP_Map.txt
-   ​5 ​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. ​ 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. ​
readme.illumina2pregs.1569544583.txt.gz · Last modified: 2019/09/27 00:36 by ignacio