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Old 03-30-2016, 04:17 PM   #1
Mike_Brown
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Default 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?
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Old 03-30-2016, 05:11 PM   #2
GenoMax
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For reference cross-posted: https://www.biostars.org/p/184179/
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