PLINK error doing a GWAS

Question

[david.badenas.01]

Hi,

I am doing the GWAS using a logistic model with covariates, using PLINK v1.9. And I get this:

PLINK v1.90b6.18 64-bit (16 Jun 2020)
Options in effect:
  --bfile imputed_breast_13
  --covar covariables.txt
  --hide-covar
  --logistic
  --out logistic_results
  --pheno breast_phenotype.txt

Start time: Thu Aug 22 19:35:25 2024

Note: --hide-covar flag deprecated.  Use e.g. "--linear hide-covar".
Random number seed: 1724348125
1031683 MB RAM detected; reserving 515841 MB for main workspace.
6662332 variants loaded from .bim file.
1886 people (0 males, 1886 females) loaded from .fam.
1886 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
--covar: 18 covariates loaded.
1885 people had missing value(s), and 1 person was not seen in the covariate file.
Before main variant filters, 1886 founders and 0 nonfounders present.
Calculating allele frequencies... done.
6662332 variants and 1886 people pass filters and QC.
**Among remaining phenotypes, 1 is a case and 0 are controls.  (1885 phenotypes
are missing.)**
**Warning: Skipping --logistic since less than two phenotypes are present.**

The first lines of my covariates:

The first lines of my phenotype:

Does anyone know what's happening and how to fix it?

Thanks in advance.

[Ram]

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[Kevin Blighe]

Hi, your pheno file should have, as its third column, an encoding of 0 (control) and 1 (case)

Kevin

[chrchang523]

Not actually true unless the --1 flag (https://www.cog-genomics.org/plink/1.9/input#pheno_encoding ) is added to the command line.

Answer 1

[chrchang523]

PLINK 2.0 supports the categorical covariate values you have in the last two columns, but PLINK 1.x does not.