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Yes you can

I ended up installing AT2 to use the PLINK files instead, does all this look alright? I did pick random samples, this was just to see if it worked. As you can see the samples labels are numbers (first column of the .fam file) The .fam file and the first column can I edit the numbers and...

thats what I did, change it manually to 2

ok so apparently converting from plink to eigensoft its not possible, you get an unusable "plain text document" .geno file no matter what this is what a proper looking .geno file looks like (the system recognizes it as a different file extension) however this is what u get when converting...

what does your .fam file says after conversion? (1st step) I get this aka no phenotype FAM001 ID001 0 0 1 -9

I think the only way to convert from PLINK to EIGENSTRAT is like its stated here https://github.com/roberta-davidson/ADMIXTURE-smartPCA-PLINK-and-EIGENSOFT?tab=readme-ov-file#readme I do also get a massive geno file , from 4,7gb to 18,8gb:)

Hi. So I installed and got qpAdm running without having too many problems but merging my files with the AADR dataset is proving to be impossible. First I tried merging the files directly in the EIGENSTRAT format(with -mergeit) but didnt get very far, then I read here about converting both the...