Issues with intersect join phenotypic, hapmap and PCA files to run a GLM+APCA association n mapping

[rm rf]

Hi dear all, I open the phenotype file in Tassel software ( in windows 10) .  Also I easily open genotypic file and run a PCA analysis on it. But when I try to intersect join the PC, Genotypic and phenotype fie for a (GLM+PCA)Association analysis), The phenotype file is not join with the PC and Genotypic file and I only see the PCs and Genotypic information after intersect join the 3 phenotypic, hapmap and PCs files. Where does the problem come from ? my phenotype datafile is in .txt format. Thank you for your help in advance

[Brandon Monier]

Hello,

Do the taxa IDs for your genotype and phenotype data match exactly?

Best,

Brandon M.