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  • Mike_Brown
    Member
    • Jan 2016
    • 13

    #1

    How to remove some columns from the output of plink

    Hello I use following command to get 012 matrix of vcf.gz
    plink --vcf test.vcf.gz --remove ID_of_miss_indv_for_plink --recode A --out TEST
    But I only want genotypes of SNPs (I want to keep the columns rs149437228_C, rs179827_A). I do not want to plink print the columns with names "._C" "._G" ,"._AC" and so on.
    Can some one help me?
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142

    #2
    For reference cross-posted: https://www.biostars.org/p/184179/

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