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readme.pregsf90 [2019/09/04 17:31]
ignacio [Quality Control (QC) for G]
readme.pregsf90 [2020/05/22 16:41] (current)
dani [Quality Control (QC) for G]
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 <​file>​OPTION hwe x</​file>​ <​file>​OPTION hwe x</​file>​
 check departure of heterozygous from Hardy-Weinberg Equilibrium.\\ check departure of heterozygous from Hardy-Weinberg Equilibrium.\\
-By default this QC is not run.\\+By defaultthis QC is not run.\\
 Optional parameter ''​x''​ set the maximum difference between observed and expected frequency\\ Optional parameter ''​x''​ set the maximum difference between observed and expected frequency\\
-default value is 0.15 as used in Wiggans et al., 2009 JDS+the default value is 0.15 as used in Wiggans et al., 2009 JDS
  
 <​file>​OPTION high_correlation x y</​file>​ <​file>​OPTION high_correlation x y</​file>​
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 Optional parameter //x// set the maximum difference in allele frequency to check pair of locus.\\ Optional parameter //x// set the maximum difference in allele frequency to check pair of locus.\\
 If no value 0.025 is used. Decrease this value to speed up calculation\\ If no value 0.025 is used. Decrease this value to speed up calculation\\
-A pair of locus is consider high correlated if the all genotypes ​were the same (0-0, 1-1, 2-2) or the opposite (0-2, 1-1, 2-0) (Wiggans et al 2009 JDS)\\ +A pair of locus is considered highly ​correlated if all the genotypes ​are the same (0-0, 1-1, 2-2) or the opposite (0-2, 1-1, 2-0) (Wiggans et al 2009 JDS)\\ 
-Optional parameter //y// can be used to set a threshold to check number of identical samples out of the number of genotypes.\\+Optional parameter //y// can be used to set a threshold to check the number of identical samples out of the number of genotypes.\\
 default values x=0.025 y=0.995 default values x=0.025 y=0.995
  
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 <​file>​OPTION exclusion_threshold x</​file>​ <​file>​OPTION exclusion_threshold x</​file>​
-Number of parent-progeny exclusions as percentage all SNP to determine wrong relationship.\\+Number of parent-progeny exclusions as percentage all SNP to determine ​the wrong relationship.\\
 default value 1  default value 1 
  
 <​file>​OPTION exclusion_threshold_snp x</​file>​ <​file>​OPTION exclusion_threshold_snp x</​file>​
-Number of parent-progeny exclusions for each locus as percentage, of pair of genotyped animals evaluated, to exclude an SNP from the analysis\\+Number of parent-progeny exclusions for each locus as percentage, of pair of genotyped animals evaluated, to exclude an SNP from the analysis\\
 default value 10  default value 10 
  
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 but they will be included for all remaining processes. **If you want to remove sex chromosomes**,​ which we do recommend, use ''​OPTION excludeCHR''​. but they will be included for all remaining processes. **If you want to remove sex chromosomes**,​ which we do recommend, use ''​OPTION excludeCHR''​.
    
-Map file need to be provided. See ''​OPTION map_file''​. However, note that sex chromosomes are not exlucded ​ +Map file need to be provided. See ''​OPTION map_file''​. However, note that sex chromosomes are not excluded ​ 
  
 <​file>​OPTION threshold_duplicate_samples x</​file>​ <​file>​OPTION threshold_duplicate_samples x</​file>​
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 <​file>​OPTION plotpca</​file>​ <​file>​OPTION plotpca</​file>​
-Plot first two principal components to look for stratification in the population. ​+Plot the first two principal components to look for stratification in the population. ​
  
 <​file>​OPTION extra_info_pca file col</​file>​ <​file>​OPTION extra_info_pca file col</​file>​
 Reads from //file// the column //col// to plot with different colors for different classes.\\ Reads from //file// the column //col// to plot with different colors for different classes.\\
-The file should ​contains ​at least one variable with different classes for each genotyped individual, and the order should match the order of the genotypes file.\\+The file should ​contain ​at least one variable with different classes for each genotyped individual, and the order should match the order of the genotypes file.\\
 Variables could be alphanumeric and separated by one o more spaces. ​ Variables could be alphanumeric and separated by one o more spaces. ​
  
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 <​file>​OPTION no_quality_control</​file> ​ <​file>​OPTION no_quality_control</​file> ​
-This option ​turn off all quality control !!!! \\+This option ​turns off all quality control !!!! \\
 Useful to speed up run when previous QC data was performed. ​ Useful to speed up run when previous QC data was performed. ​
  
readme.pregsf90.txt · Last modified: 2020/05/22 16:41 by dani