Differences

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--- ped [2011/06/07 17:19] – 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 64: / 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 ====
+  * Each line of the MAP file describes a single marker and must contain exactly 4 columns:
+    * chromosome (1-22, X, Y, MT or 0 if unplaced)
+    * rs# or snp identifier
+    * Genetic distance (morgans) (missing: 0)
+    * Base-pair position (bp units) (Base-pair positions are expected to correspond to positive integers within the range of typical human chromosome sizes)
+  * 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 77: / Line 90: @@
 ==== Example ====
+  * PED files:
 <code>
 FAM001  1  0 0  1  2  A A  G G  A C
@@ Line 86: / Line 100: @@
 1 0 0 2   1   A A    A A    A A    A A    A A
 1 0 0 2   1   A C    A C    A C    A C    A C
+</code>
+  * MAP files:
+<code>
+  rs123456  0  1234555
+  rs234567  0  1237793
+  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 =====