Changes between Version 11 and Version 12 of ImputationPipeline


Ignore:
Timestamp:
Nov 23, 2010 11:13:51 AM (11 years ago)
Author:
a.kanterakis
Comment:

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  • ImputationPipeline

    v11 v12  
    144144
    145145==== Source code ====
    146  http://www.bbmriwiki.nl/svn/Imputation/impute2/ConvertBedBimFamToPedMap.py
     146  http://www.bbmriwiki.nl/svn/Imputation/impute2/ConvertBedBimFamToPedMap.py
     147
     148=== DividePedMapToChromosomes ===
     149This script divides a pair of PED and MAP files to chromosomes by using plink (http://pngu.mgh.harvard.edu/~purcell/plink/).
     150
     151==== Parameters ====
     152 * path to plink (example: /Users/alexandroskanterakis/Tools/plink/plink-1.07-mac-intel/plink) 
     153 * path to map file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.map) 
     154 * path to ped file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.ped) 
     155 * Directory where files will be exported (example: /Users/alexandroskanterakis/Data/Finnish_cohort/DividedChromosomes) 
     156 * Suffix of the exported files (example: output_) 
     157
     158==== Example ====
     159
     160{{{
     161#!div style="font-size: 80%"
     162Code highlighting:
     163  {{{#!python
     164DividePedMapToChromosomes(
     165        plink_path= "/Users/alexandroskanterakis/Tools/plink/plink-1.07-mac-intel/plink",
     166        map_path="/Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.map",
     167        ped_path="/Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.ped",
     168        output_path="/Users/alexandroskanterakis/Data/Finnish_cohort/DividedChromosomes",
     169        suffix="output_")
     170  }}}
     171}}}
     172
    147173== BEABLE pipeline ==
    148174