**30**wrote:

Hello,

I am trying to run a GWAS with linear regression using Plink2. I call for linear however, the moment plink2 detects a binary phenotype it switches to logistic. Has any one else faced this issue? Is there a work around?

Plink2:

```
$plink2 --pfile $pfile \
--pheno $pheno_file \
--pheno-name $pheno_name \
--keep $samples_list \
--maf 0.01 \
--linear cols=+a1freq,+machr2 \
--vif 999 \
--covar $pheno_file \
--covar-name $covar_list \
--covar-variance-standardize \
--memory 19000 \
--threads 10 \
--adjust \
--out "$outdir"
Log:
LINK v2.00a2LM 64-bit Intel (29 Apr 2019) www.cog-genomics.org/plink/2.0/
(C) 2005-2019 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to /scratch/scratch3/op_genomic2/anoop/TAA_20200903/5_full_HARE_15pcs/3_assoc_glm_lin/out_plinkLIN1.log.
Options in effect:
--adjust
--covar pheno.tsv
--covar-name AGE, GENDER, PC1, PC2, PC3, PC4, PC5
--covar-variance-standardize
--glm cols=+a1freq,+machr2
--keep pheno.tsv
--maf 0.01
--memory 19000
--out plink_out
--pfile chr10
--pheno pheno.tsv
--pheno-name Pheno
--threads 10
--vif 999
--
1 binary phenotype loaded
--glm logistic regression on phenotype 'Pheno': 0%^H^H2%^H^H5%^H^H7%^H^H10%^H^H^H12%^H^H^H14%^H^H^H16%^H^H^H18%^H^H^H21%^H^H^H23%^H^H^H26%^H^H^H28%^H^H^H31%^H^H^H33%^H^H^H36%^H^H^H39%^H^H^H41%^H^H^H44%^H^H^H47%^H^H^H50%^H^H^H52%^H^H^H55%^H^H^H57%^H^H^H59%^H^H^H62%^H^H^H64%^H^H^H67%^H^H^H70%^H^H^H72%^H^H^H74%^H^H^H76%^H^H^H79%^H^H^H81%^H^H^H84%^H^H^H86%^H^H^H88%^H^H^H91%^H^H^H93%^H^H^H96%^H^H^H99%^H^H^Hdone.
```

Seems like a bug, but the manual is a little ambiguous so it might be by design. Any suggestions would be greatly appreciated.

Thanks!

Thanks chrchang523.

I understand this, I am however trying to analyze a large dataset compared my Computational resources and logistic regression is a lot more expensive.

I will try the hack, thanks!

30If you don't have missing genotypes, the 'cc-residualize' modifier implemented in July 2020 is a better way to trade off a little accuracy for speed.

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