Differences

This shows you the differences between two versions of the page.

--- ped [2011/06/07 17:28] – heidi
+++ ped [2011/06/08 09:42] (current) – heidi
@@ Line 19: / Line 19: @@
   * Unix
 \\
@@ Line 26: / Line 27: @@
 ===== Data type handled =====
   * diploid
-  * AFLP
+  * SNP
-  * MICROSAT
-  * Standard
 \\
@@ Line 65: / Line 65: @@
 If specially specified following columns can be missing:
   * ''Family ID''
-    * ''Individual ID''
+  * ''Individual ID''
-    * ''Paternal ID'' and ''Maternal ID''
+  * ''Paternal ID'' and ''Maternal ID''
-    * ''Sex''
+  * ''Sex''
-    * ''Phenotype''
+  * ''Phenotype''
 \\
-===== MAP files =====
+==== MAP files ====
   * Each line of the MAP file describes a single marker and must contain exactly 4 columns:
-    * chromosome (1-22, X, Y or 0 if unplaced)
+    * chromosome (1-22, X, Y, MT or 0 if unplaced)
     * rs# or snp identifier
     * Genetic distance (morgans) (missing: 0)
@@ Line 79: / Line 82: @@
   * The MAP file must contain as many markers as are in the PED file.
   * The markers in the PED file do not need to be in genomic order: (i.e. the order MAP file should align with the order of the PED file markers).
+\\
@@ Line 102: / Line 107: @@
   rs224534  0  -1237697
   rs233556  0  1337456
+</code>
+<code>
+    snp1   0   1000
+X    snp2   0   1000
+Y    snp3   0   1000
+XY   snp4   0   1000
+MT   snp5   0   1000
 </code>
 \\
 ===== How to cite =====
 Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81.