GWAS in Plink - phenotype file format

Question

[SGMS]

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

[Ram]

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 written proof anywhere.

[SGMS]

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

Answer 1

[chrchang523]

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.

[bjwiley23]

The documentation for 1.07 doesn't have this tidbit. https://zzz.bwh.harvard.edu/plink/dist/plink-doc-1.07.pdf

[chrchang523]

I don’t have control over the 1.07 documentation. I’ve done what I can.

[Kumar]

please let me know what should be the format of phenotype as input file at plink.

[chrchang523]

For plink 2.0, there's an example at https://www.cog-genomics.org/plink/2.0/input#pheno .