Question: PLINK unable to read covariate file
0
gravatar for zichunxu0824
4 months ago by
zichunxu08240 wrote:

Hello everyone, I am doing a GWAS analysis by plink 1.9. When I upload my covariate file, it reads

Ignoring --covar since no commands reference the covariates

I have double-checked my covariate file and it is in the right format (as it works as a phenotype file). I have also checked the value of the covariate file (with R) and it is indeed numeric. Here it is my command:

--bfile ../genotype_all/qc_1 --pheno ../phenotype/weight --covar test_covar.txt --covar-number 1 --assoc

and here it is the log:

Logging to plink.log.
Options in effect:
  --assoc
  --bfile ../genotype_all/qc_1
  --covar test_covar.txt
  --covar-number 1
  --pheno ../phenotype/weight

64266 MB RAM detected; reserving 32133 MB for main workspace.
449792 variants loaded from .bim file.
488371 people (223470 males, 264803 females, 98 ambiguous) loaded from .fam.
Ambiguous sex IDs written to plink.nosex .
486613 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Warning: Ignoring --covar since no commands reference the covariates.

Can anyone tell what is wrong? Thank you very much for your help!

snp plink gwas • 229 views
ADD COMMENTlink modified 4 months ago by chrchang5237.1k • written 4 months ago by zichunxu08240

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
code_formatting

ADD REPLYlink written 4 months ago by RamRS28k
2
gravatar for chrchang523
4 months ago by
chrchang5237.1k
United States
chrchang5237.1k wrote:

You're using --assoc, which is an obsolete command that does not take covariates into account. Use --linear/--logistic instead.

ADD COMMENTlink written 4 months ago by chrchang5237.1k

It works! Thank you!

ADD REPLYlink written 4 months ago by zichunxu08240
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