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readme.seekparentf90 [2019/05/29 12:58]
ignacio [Optional arguments]
readme.seekparentf90 [2020/03/31 16:00] (current)
ignacio
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   Program ''​SeekParentF90''​ detect parent-offspring incompatibilities based on   Program ''​SeekParentF90''​ detect parent-offspring incompatibilities based on
- ​counts of Mendelian conflicts, as described in: Hayes 2010 JAS+ ​counts of Mendelian conflicts, as described in: Hayes 2011 JDS
  and Wiggans et al 2010 JDS  and Wiggans et al 2010 JDS
  
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 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:\\
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 </​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.seekparentf90.1559134701.txt.gz ยท Last modified: 2019/05/29 12:58 by ignacio