Hi, I have a plink alternative phenotype file with the following format:
FID IID Phenotype
1 2 1
1 3 0
..
As outlined in the plink documentation https://zzz.bwh.harvard.edu/plink/data.shtml#pheno
However, when I run the following command :
plink --bfile ../Plink_Files/plink --logistic --adjust --pheno ../Pheno_Files/pheno.txt --all-pheno --covar ../Cov_Files/pheno.txt --covar-number 2-4 --allow-no-sex --out Results/pheno
I get the following error message:
4768 people (0 males, 0 females, 4768 ambiguous) loaded from .fam.
Ambiguous sex IDs written to Results/Fibroids.nosex .
397 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
--covar: 3 out of 11 covariates loaded.
1271 people were not seen in the covariate file.
Before main variant filters, 4768 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.943943.
94036 variants and 4768 people pass filters and QC.
Among remaining phenotypes, 0 are cases and 397 are controls. (4371 phenotypes
are missing.)
397 phenotype values present after --pheno.
Pheno has 0 cases, 397 controls, and 4371 missing phenotypes.
Which implies that the phenotype file is being read where the rows are phenotypes not the columns because it says the phenotypes are missing. I am not sure why that would be since the phenotype file matches the plink format that I found online. Any help in fixing this error would be greatly appreciated!