readme.pregsf90
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readme.pregsf90 [2019/09/04 17:31] – [Quality Control (QC) for G] ignacio | readme.pregsf90 [2020/11/10 19:25] – [Input files] dani | ||
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- | First SNP in the Map fiel corresponds to first SNP in genotype file, and so on. | + | The first SNP in the Map file corresponds to the first SNP in the genotype file, and so on. |
- | Other alphanumeric | + | Other alphanumeric |
If '' | If '' | ||
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< | < | ||
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 '' | Optional parameter '' | ||
- | 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 |
< | < | ||
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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 | + | A pair of locus is considered highly |
- | 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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< | < | ||
- | Number of parent-progeny exclusions as percentage all SNP to determine wrong relationship.\\ | + | Number of parent-progeny exclusions as percentage all SNP to determine |
default value 1 | default value 1 | ||
< | < | ||
- | 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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but they will be included for all remaining processes. **If you want to remove sex chromosomes**, | but they will be included for all remaining processes. **If you want to remove sex chromosomes**, | ||
- | Map file need to be provided. See '' | + | Map file need to be provided. See '' |
< | < | ||
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< | < | ||
- | 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. |
< | < | ||
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 | + | The file should |
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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< | < | ||
- | This option | + | This option |
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: 2024/03/25 18:22 by 127.0.0.1