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Plink Problem Reading The Covariate File

Hi,

I am conducting a eQTL analysis using Plink. Though I am providing a covariate file, Plink is not reading this file. It says "Reading 0 covariates from [ covar.dat ] with nonmissing values for 0 individuals". Has anyone come across such problem?

Thanks,

plink eqtl
• 8,442 views • link
updated by Maxime Lamontagne Maxime Lamontagne • written by geetha.r.v • geetha.r.v

Please provide sample covariate file: head covar.dat > sample_covar.dat

• 72 views • link
written by zx8754 zx8754

I have one covariate, "AGE" which is as follows: AGE 91 91 33 47 43

• 1 views • link
written by geetha.r.v • geetha.r.v

I corrected the covariate file by including the FID, IID and then AGE. Now it reads and seems to work fine but in the .assoc.linear file, now I see only AGE, there is no ADD which represents the test for the SNP-phenotype association after controlling for the covariate.

• 0 views • link
written by geetha.r.v • geetha.r.v

1 answer

Your covariate file need to be like: 

FID      IID       Age   Heigh
Family1  Subject1  54    1.80
Family2  Subject2  63    1.50

YOur FID and IID need to be the same in the ped or fam file.

• 67 views • link
written by Maxime Lamontagne Maxime Lamontagne

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