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99 bytes added ,  09:18, 5 December 2010
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   awk '{print $3}' orig.hap | cut -c${first}-${last} > region.hap
 
   awk '{print $3}' orig.hap | cut -c${first}-${last} > region.hap
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The created reference files are in MaCH format. You do NOT need to turn on --hapmapFormat option.
    
== Do I always have to sort the pedigree file by marker position?  ==
 
== Do I always have to sort the pedigree file by marker position?  ==
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