Merge .bed files from different samples using PLINK

Question

[yangyx117]

Hi all,

I have 10 separate .bed/.bim/.fam files. These files have the same set of SNPs but from different samples. How can I merge these files into one using PLINK? Seems like PLINK's '--merge' function can only merge files with different SNPs from same samples?

Many thanks!

Answer 1

[zx8754]

--merge-list <filename> flag should work, see:

• https://www.cog-genomics.org/plink/1.9/data#merge_list

Something like:

plink --merge-list myFile.txt --make-bed --out myMergedOut

Where myFile.txt is:

gwas1.bed gwas1.bim gwas1.fam
gwas2.bed gwas2.bim gwas2.fam
...

or

gwas1
gwas2
...