Question: PLINK vcf to binary files error: Unused command line option: --vcf
gravatar for jon.klonowski
16 months ago by
jon.klonowski70 wrote:

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

genomics plink vcf • 1.3k views
ADD COMMENTlink modified 16 months ago by chrchang5237.1k • written 16 months ago by jon.klonowski70

Where's the command you're running? All I see is the input and directed output.

ADD REPLYlink written 16 months ago by ggman80
gravatar for chrchang523
16 months ago by
United States
chrchang5237.1k wrote:

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

ADD COMMENTlink written 16 months ago by chrchang5237.1k

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

ADD REPLYlink written 16 months ago by jon.klonowski70

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?

ADD REPLYlink written 3 months ago by curls0

oh i know why, becuase is the first thing that comes up on google... not sure why the old version is the first on the search.

ADD REPLYlink written 16 months ago by jon.klonowski70
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