PLINK vcf to binary files error: Unused command line option: --vcf
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3.6 years ago
jon.klonowski ▴ 130

I am trying to make bim bam bed files from a vcf file but i keep getting an cryptic error:

plink --vcf filename.vcf.gz --recode --out test_out


* Unused command line option: --vcf
*
Unused command line option: filename.vcf.gz

I tried just using --file and that throws an error I dont know what it means..... i thought maybe it give me that error because i didnt specify I am giving it a vcf.

plink --file finename.vcf.gz --recode --out test


ERROR: A problem with line 1 in [ filename.vcf.gz.ped ] Expecting 5 + 2 * 456042 = 912089 columns, but found 6

I am guessing I need to use the --file flag and put all the genotypes.... how would I put the genotypes from a vcf into a ped file? The samples are all unrelated affected patients so I created my own PED file by: fam id, sample id = sample number mother, father, sex = 0 phenotpe = 2

plink vcf genomics • 3.5k views
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Where's the command you're running? All I see is the input and directed output.

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3.6 years ago

--vcf requires plink 1.9; you appear to be using plink 1.07.

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No idea how I had plink1.07. meh. thank you so much

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I am trying to get bed/bim/fam files for structure analysis. I have plink 1.07 which does not work for conversion of VCF to plink bed format. After reading your comment, I downloaded plink2, however, it does not work. I tried to uninstall plink 1.07 but I also could not do that. I am new on command line. I searched but I could not find a way to do that. I was wondering if you have any idea to uninstall older version and install new version of plink?

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oh i know why, becuase http://zzz.bwh.harvard.edu/plink/download.shtml is the first thing that comes up on google... not sure why the old version is the first on the search.