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--- readme.pregsf90 [2019/07/26 21:52] – [Input files] ignacio
+++ readme.pregsf90 [2019/09/04 17:31] – [Quality Control (QC) for G] ignacio
@@ Line 89: / Line 89: @@
 //SNP_ID// - identification of the SNP (alphanumeric) \\
 //CHR// - chromosome number (numeric), starting from 1 \\
-//POS// - position (bp) \\
+//POS// - position bp (numeric) \\
 Extra columns are possible \\
@@ Line 101: / Line 101: @@
 If ''OPTION saveCleanSNPs'' is present fields are output.
-<file>OPTION chrinfo file </file>
-OLD OPTION DEPRECATED \\
-Read SNP map information from //file//.\\
-Useful for check for Mendelian conflicts and HWE (with also ''OPTION sex_chr'') and for GWAS (see ''PostGSF90'' program)
-Format, all numeric variables: //snp order , chromosome, position// (bp).
-//snp order// corresponds to the index number of the snp, in the sorted map by chromosome and position
-//chromosome// should be only numbers and starting from 1
-First line in file corresponds to first SNP in genotype file, and so on.
-Other alphanumeric field are optional.
-If ''OPTION saveCleanSNPs'' is present fields are output.
 =====Output files=====
@@ Line 290: / Line 272: @@
 <file>OPTION excludeCHR n1 n2 n3 ...</file>
 Exclude all SNP from chromosomes //n1 n2 n3// ...\\
-Map file need to be provided. See ''OPTION chrinfo''
+Map file need to be provided. See ''OPTION map_file''
 <file>OPTION includeCHR n1 n2 n3 ...</file>
 Include all SNP from chromosomes //n1 n2 n3// ...\\
-Map file need to be provided. See ''OPTION chrinfo''
+Map file need to be provided. See ''OPTION map_file''
 <file>OPTION excludeSample n1 n2 n3 ...</file>
@@ Line 302: / Line 284: @@
 <file>OPTION sex_chr n</file>
 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''.
-Map file need to be provided. See ''OPTION chrinfo''. 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 exlucded
 <file>OPTION threshold_duplicate_samples x</file>
@@ Line 376: / Line 358: @@
 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.
@@ Line 689: / Line 670: @@
 OPTION readGmA22 [file]
 </file>
+=====DEPRECATED OPTIONS=====
+<file>OPTION chrinfo file </file> \\
+Read SNP map information from //file//.\\
+Useful for check for Mendelian conflicts and HWE (with also ''OPTION sex_chr'') and for GWAS (see ''PostGSF90'' program)
+Format, all numeric variables: //snp order , chromosome, position// (bp).
+//snp order// corresponds to the index number of the snp, in the sorted map by chromosome and position
+//chromosome// should be only numbers and starting from 1
+First line in file corresponds to first SNP in genotype file, and so on.
+Other alphanumeric field are optional.
+If ''OPTION saveCleanSNPs'' is present fields are output.