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readme.pregsf90 [2019/07/26 21:57] ignacio [Input files] |
readme.pregsf90 [2020/05/22 16:41] 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 default, this 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 a percentage, of pair of genotyped animals evaluated, to exclude an SNP from the analysis\\ |
default value 10 | default value 10 | ||
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<file>OPTION sex_chr n</file> | <file>OPTION sex_chr n</file> | ||
Chromosomes number equal or greater than //n// are not consider autosomes.\\ | Chromosomes number equal or greater than //n// are not consider autosomes.\\ | ||
- | If selected this option, sex chromosomes will not be used for checking parent-progeny Mendelian conflicts and HWE\\ | + | If selected this option, sex chromosomes will not be used for checking parent-progeny Mendelian conflicts, HWE and heritability of gene content\\ |
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. | ||
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The test is useful for homogenous populations (breeds) but theory does not hold for crossbred animals. | The test is useful for homogenous populations (breeds) but theory does not hold for crossbred animals. | ||
This test uses explicitly inv(A22) so it is not suitable for very large populations. | This test uses explicitly inv(A22) so it is not suitable for very large populations. | ||
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