We have some difficulties about using 23andMe data on plink. We have raw 23andMe snp data for each individual (total of 756). We converted each individual file to binary fileset .bed,.bim, .fam via plink.
plink --23file $file --out $a
After creating binary set for each individual, we converted them into .map and .bed format.
plink --bfile binary_filesets --a2-allele ../All.vcf 4 3 '#' --recode --out $a
Then, we want to collect info of all individuals into same .bed file( or binary fileset.)
plink --file genom0 --merge-list ../filesets3.txt --make-bed --out ../combined/combdata
We assume --merge-list does this job, however, it does overwrite one individual into another. It doesn't create many individuals x info (matrix-like) data. How could we obtain one combined binary fileset for many individuals?