How to remove some columns from the output of plink

Mike_Brown · 03-30-2016, 04:17 PM

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 · 03-30-2016, 05:11 PM

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

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03-30-2016, 04:17 PM	#1
Mike_Brown Member Location: usa Join Date: Jan 2016 Posts: 13	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?

03-30-2016, 05:11 PM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	For reference cross-posted: https://www.biostars.org/p/184179/