Question: GWAS in Plink - phenotype file format
gravatar for SGMS
20 months ago by
European Union
SGMS70 wrote:

Hi everyone,

My question may be too simple for experienced PLINK users, yet I cannot find the simplest answers anywhere online.

I was looking for a sample analysis in plink to see how a GWAS is actually run as I am a super new user.

I have created .ped and .map files using:

vcftools --vcf chr21.vcf --chr 21 --from-bp 9411245 --to-bp 9411245 --out results --plink

and have also tried using the plink command:

../plink_linux_x86_64/plink --double-id --vcf chr21.vcf.gz --chr 21 --from-bp 9411245 --to-bp 9411245 --recode --out out

which provided me with a .map, .ped and .nosex outputs.

I have a text file with the columns of the phenotypes for which I need to run my GWAS but the problem is I do not know what the phenotype file should exactly have or whether I should use one of the above files in my GWAS run. My pheno.txt looks like this:

Phenotype1     Phenotype 2    Phenotype 3
0.969740676 1.092626777 1.467815889
0.751133434 -0.231977679    0.318320143

Now I used the following command to run GWAS:

../plink_linux_x86_64/plink --double-id --vcf chr21.vcf --pheno pheno.txt --mpheno 3 --linear --out gwas_results

Could someone give me a clue please??

Thanks a lot in advance

phenotype plink snps gwas • 2.8k views
ADD COMMENTlink modified 20 months ago by zx87549.3k • written 20 months ago by SGMS70

IIRC the phenotype file is just IID, FID and the phenotype column from the traditional PED format. I'm trying to find solid support for this, but while I can recall seeing it a while ago, I can't seem to find a written proof anywhere.

ADD REPLYlink written 20 months ago by RamRS27k

Thanks a lot! Exactly, it's so simple but I couldn't find a source saying that precisely.

ADD REPLYlink written 20 months ago by SGMS70
gravatar for chrchang523
20 months ago by
United States
chrchang5237.1k wrote:

This is explained at the beginning of the documentation for --pheno:

--pheno causes phenotype values to be read from the 3rd column of the specified space- or tab-delimited file, instead of the .fam or .ped file. The first and second columns of that file must contain family and within-family IDs, respectively.

ADD COMMENTlink modified 20 months ago by zx87549.3k • written 20 months ago by chrchang5237.1k
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