Will Plink and GCTA match and reorder sample order?
Will Plink and GCTA will match and reorder the sample order from covariates or phenotypes files to genotypes file sample order?
plink --bfile ${AD_geno}_1 --covar Covariates_AVD.txt --write-covar --dummy-coding${GCTA} --grm kinship_AVD --bfile ${AD_geno}_1 --pheno Pheno_AVD.txt
Today, I realized that the sample order in Covariates_AVD.txt and Pheno_AVD.txt are different with ${AD_geno}_1.fam. Does it matter? I have finished this project several month ago. Afraid to come back.
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