I have multiple plink genome files that each contain only one individual and would like to combine them into one set (bim/bed/fam) that contains multiple individuals WITHOUT merging their DNA together, however when I have tried I think I am not doing it correctly and have created a BrundleFly (some will get this reference).

Here is some information about what I have done so far:

The source of these files are 23andMe raw data text files. I convert them to plink format with the following command:

plink --23file file.txt SMITH AGENT M --out agentSmithPlink

• This seems to work fine. Then I merge with other files similarly created using the following command:

plink --bfile agentSmithPlink --merge-list list.txt --make-bed --out combinedPlink

• The file list.txt is formatted as follows for simplification:

secondPerson.bed secondPerson.bim secondPerson.fam

This also seems to work, but the software I put the combinedPlink file through leads me to believe a small mess was created.

• I've made sure to create unique individual IDs for each person
• I've tried using --snps-only no-DI when converting from 23andMe to plink

Any help would be greatly appreciated.