User Tools

Site Tools


readme.seekparentf90

Differences

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

Link to this comparison view

Both sides previous revision Previous revision
Last revision Both sides next revision
readme.seekparentf90 [2020/03/16 23:50]
ignacio [Summary]
readme.seekparentf90 [2020/03/31 16:00]
ignacio
Line 132: Line 132:
  
 If more than one chip is used then the number of SNP in common for two samples (base on both chips) will be used for check conflict and for discovering of parents. ​ If more than one chip is used then the number of SNP in common for two samples (base on both chips) will be used for check conflict and for discovering of parents. ​
-====Other options==== 
-<​file>​--only_in_common</​file>​ 
-Select the SNP in common between all chips to be used in the analyses ​ 
  
- 
-<​file>​--include_snp <​file></​file>​ 
-Only the list of SNP names in //file// will be included in the analyses 
- 
-<​file>​--exclude_snp <​file>​ </​file>​ 
-The list of SNP names in //file// will be excluded from analyses 
- 
- 
-<​file>​--include_chr <n1 n2.. n></​file>​ 
-Only SNP in Chromosomes //n1 n2, etc// will be included in the analyses 
-  
-<​file>​--exclude_chr <n1 n2.. n></​file>​ 
-SNP in Chromosomes //n1 n2, etc// will be excluded from analyses 
-  
-<​file>​--chr_x <​n></​file>​ 
-Indicate that the //n// chromosome ​ is the X chromosome and then SNP will be excluded from check of parent-progeny conflicts and parentage discovering 
 ====Example==== ====Example====
 Consider a genotype file with 4 samples and 3 chips with the following number of SNP:\\ Consider a genotype file with 4 samples and 3 chips with the following number of SNP:\\
Line 211: Line 192:
 </​file>​ </​file>​
   ​   ​
 +
 +====Other options====
 +<​file>​--only_in_common</​file>​
 +Select the SNP in common between all chips to be used in the analyses ​
 +
 +
 +<​file>​--include_snp <​file></​file>​
 +Only the list of SNP names in //file// will be included in the analyses
 +
 +<​file>​--exclude_snp <​file>​ </​file>​
 +The list of SNP names in //file// will be excluded from analyses
 +
 +
 +<​file>​--include_chr <n1 n2.. n></​file>​
 +Only SNP in Chromosomes //n1 n2, etc// will be included in the analyses
 + 
 +<​file>​--exclude_chr <n1 n2.. n></​file>​
 +SNP in Chromosomes //n1 n2, etc// will be excluded from analyses
 + 
 +<​file>​--chr_x <​n></​file>​
 +Indicate that the //n// chromosome ​ is the X chromosome and then SNP will be excluded from check of parent-progeny conflicts and parentage discovering
    
 =====Output files===== =====Output files=====
readme.seekparentf90.txt ยท Last modified: 2021/11/18 20:14 by ignacio