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--- readme.pregsf90 [2019/09/04 17:31] – [Quality Control (QC) for G] ignacio
+++ readme.pregsf90 [2021/07/28 19:24] – dani
@@ Line 86: / Line 86: @@
 Useful for check for Mendelian conflicts and HWE (with also ''OPTION sex_chr'') and for GWAS (see ''PostGSF90'' program)
-The //file// should has a header with the following column names:\\
+The //file// should have a header with the following column names:\\
 //SNP_ID// - identification of the SNP (alphanumeric) \\
 //CHR// - chromosome number (numeric), starting from 1 \\
@@ Line 95: / Line 95: @@
-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 field are optionals.
+Other alphanumeric fields are optional.
 If ''OPTION saveCleanSNPs'' is present fields are output.
@@ Line 230: / Line 230: @@
 <file>OPTION hwe x</file>
 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\\
-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>
@@ Line 239: / Line 239: @@
 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\\
-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
@@ Line 256: / Line 256: @@
 <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
 <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
@@ Line 287: / Line 287: @@
 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>
@@ Line 294: / Line 294: @@
 <file>OPTION high_threshold_diagonal_g x</file>
-Check and remove individuals with extreme high diagonals in the genomic relationship matrix.\\
+Check and provide a list of individuals with extreme high diagonals in the genomic relationship matrix.\\
 If optional //x// is present set the threshold\\
 default value 1.6
 <file>OPTION low_threshold_diagonal_g x</file>
-Check and remove individuals with extreme low diagonals in the genomic relationship matrix.\\
+Check and provide a list of individuals with extreme low diagonals in the genomic relationship matrix.\\
 If optional //x// is present set the threshold\\
 default value 0.7
 <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>
 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.
@@ Line 345: / Line 345: @@
 <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.