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--- readme.seekparentf90 [2019/05/29 12:57] – [Optional arguments] ignacio
+++ readme.seekparentf90 [2020/03/31 16:00] – ignacio
@@ Line 12: / Line 12: @@
   Program ''SeekParentF90'' detect parent-offspring incompatibilities based on
- counts of Mendelian conflicts, as described in: Hayes 2010 JAS
+ counts of Mendelian conflicts, as described in: Hayes 2011 JDS
  and Wiggans et al 2010 JDS
@@ Line 116: / Line 116: @@
 <file>--find_duplicate <file> [thr]</file>
-check for duplicate samples only for individuals in the specified <file> across the full genotype file. \\
+check for duplicate samples only for individuals in the specified //file// across the full genotype file. \\
 Optional parameter //thr// changes the default threshold to identify duplicate samples (default 0.9)
@@ Line 132: / Line 132: @@
 If more than one chip is used then the number of SNP in common for two samples (base on both chips) will be used for check conflict and for discovering of parents.
-====Other options====
-<file>--only_in_common</file>
-Select the SNP in common between all chips to be used in the analyses
-<file>--include_snp <file></file>
-Only the list of SNP names in //file// will be included in the analyses
-<file>--exclude_snp <file> </file>
-The list of SNP names in //file// will be excluded from analyses
-<file>--include_chr <n1 n2.. n></file>
-Only SNP in Chromosomes //n1 n2, etc// will be included in the analyses
-<file>--exclude_chr <n1 n2.. n></file>
-SNP in Chromosomes //n1 n2, etc// will be excluded from analyses
-<file>--chr_x <n></file>
-Indicate that the //n// chromosome  is the X chromosome and then SNP will be excluded from check of parent-progeny conflicts and parentage discovering
 ====Example====
 Consider a genotype file with 4 samples and 3 chips with the following number of SNP:\\
@@ Line 211: / Line 192: @@
 </file>
+====Other options====
+<file>--only_in_common</file>
+Select the SNP in common between all chips to be used in the analyses
+<file>--include_snp <file></file>
+Only the list of SNP names in //file// will be included in the analyses
+<file>--exclude_snp <file> </file>
+The list of SNP names in //file// will be excluded from analyses
+<file>--include_chr <n1 n2.. n></file>
+Only SNP in Chromosomes //n1 n2, etc// will be included in the analyses
+<file>--exclude_chr <n1 n2.. n></file>
+SNP in Chromosomes //n1 n2, etc// will be excluded from analyses
+<file>--chr_x <n></file>
+Indicate that the //n// chromosome  is the X chromosome and then SNP will be excluded from check of parent-progeny conflicts and parentage discovering
 =====Output files=====