Changes between Version 11 and Version 12 of GoNL_Immunochip_Data_Preparation


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Timestamp:
Jul 1, 2011 4:20:56 PM (13 years ago)
Author:
laurent
Comment:

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  • GoNL_Immunochip_Data_Preparation

    v11 v12  
    1212The only tool to have an easy (yet not completely correct) conversion from PED to VCF is the beta version of PLINK/Seq available -along with instructions- here: http://www.broadinstitute.org/gsa/wiki/index.php/Converting_ped_to_vcf
    1313
     14 * plink108 --file in_plink_filename --recode-vcf --out out_filename
     15
    1416This pre-compiled version can only be run on Linux64 machines and some dependency problems may occur.
    1517
    1618The result here is a VCF tool that contains all
    17 
    1819== Correct the initial VCF file ==
    1920The 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.