Changes between Version 8 and Version 9 of ImputationPipeline


Ignore:
Timestamp:
Nov 23, 2010 10:42:17 AM (11 years ago)
Author:
a.kanterakis
Comment:

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  • ImputationPipeline

    v8 v9  
    111111
    112112== IMPUTE pipeline ==
     113=== ConvertBedBimFamToPedMap ===
     114This 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:
    113115
    114 TODO: paste shell script descriptions of each step.
     116 * /path/to/FILE1.maf05.bed
     117 * /path/to/FILE1.maf05.bim
     118 * /path/to/FILE1.maf05.fam
    115119
     120Then the parameter value should be: /'''path/to/FILE1.maf05'''
     121
     122''''''Note: creates rather big plink.ped files
     123
     124==== Parameters ====
     125
     126 * Path to plink executable (example: /Users/alexandroskanterakis/Tools/plink/plink-1.07-mac-intel/plink) 
     127 * Path to BED, BIM, FAM file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05) 
     128 * Filename of exported PED file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.ped) 
     129 * Filename of exported MAP file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.map) 
    116130== BEABLE pipeline ==
    117131