Changes between Version 11 and Version 12 of ImputationPipeline

Timestamp:

Nov 23, 2010 11:13:51 AM (15 years ago)

Author:

a.kanterakis

Comment:

--

ImputationPipeline

@@ -144 +144 @@
 
 ==== Source code ====
- http://www.bbmriwiki.nl/svn/Imputation/impute2/ConvertBedBimFamToPedMap.py
+  http://www.bbmriwiki.nl/svn/Imputation/impute2/ConvertBedBimFamToPedMap.py
+
+=== DividePedMapToChromosomes ===
+This script divides a pair of PED and MAP files to chromosomes by using plink (http://pngu.mgh.harvard.edu/~purcell/plink/).
+
+==== Parameters ====
+ * path to plink (example: /Users/alexandroskanterakis/Tools/plink/plink-1.07-mac-intel/plink) 
+ * path to map file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.map) 
+ * path to ped file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.ped) 
+ * Directory where files will be exported (example: /Users/alexandroskanterakis/Data/Finnish_cohort/DividedChromosomes) 
+ * Suffix of the exported files (example: output_) 
+
+==== Example ====
+
+{{{
+#!div style="font-size: 80%"
+Code highlighting:
+  {{{#!python
+DividePedMapToChromosomes(
+        plink_path= "/Users/alexandroskanterakis/Tools/plink/plink-1.07-mac-intel/plink",
+        map_path="/Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.map",
+        ped_path="/Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.ped",
+        output_path="/Users/alexandroskanterakis/Data/Finnish_cohort/DividedChromosomes",
+        suffix="output_")
+  }}}
+}}}
+
 == BEABLE pipeline ==