Changes between Version 8 and Version 9 of ImputationPipeline

Timestamp:

Nov 23, 2010 10:42:17 AM (14 years ago)

Author:

a.kanterakis

Comment:

--

ImputationPipeline

@@ -111 +111 @@
 
 == IMPUTE pipeline ==
+=== ConvertBedBimFamToPedMap ===
+This script converts BED, BIM, FAM files to PED and MAP by using plink. The "Path to BED, BIM, FAM file" parameter should contain the path and the suffix of these files. For example if the files are:
 
-TODO: paste shell script descriptions of each step.
+ * /path/to/FILE1.maf05.bed
+ * /path/to/FILE1.maf05.bim
+ * /path/to/FILE1.maf05.fam
 
+Then the parameter value should be: /'''path/to/FILE1.maf05'''
+
+''''''Note: creates rather big plink.ped files
+
+==== Parameters ====
+
+ * Path to plink executable (example: /Users/alexandroskanterakis/Tools/plink/plink-1.07-mac-intel/plink) 
+ * Path to BED, BIM, FAM file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05) 
+ * Filename of exported PED file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.ped) 
+ * Filename of exported MAP file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.map) 
 == BEABLE pipeline ==