Changes between Version 12 and Version 13 of GoNL_Immunochip_Data_Preparation


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Timestamp:
Jul 1, 2011 4:21:10 PM (13 years ago)
Author:
laurent
Comment:

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  • GoNL_Immunochip_Data_Preparation

    v12 v13  
    1515
    1616This pre-compiled version can only be run on Linux64 machines and some dependency problems may occur.
    17 
    18 The result here is a VCF tool that contains all
    1917== Correct the initial VCF file ==
    2018The initial VCF file produced by PLINK 1.08 does contain the right information, however it is not actually in VCF format. The problem here is that PLINK files specify the Ref/Alt alleles relative to the dataset where VCF specifies the Ref/Alt alleles relative to the Human Genome Reference it is aligned on. To correct this VCF file, it is necessary to modify the initial VCF file so that the alleles are relative to the Human Genome Reference and not the dataset anymore.