Plink: Number of Samples reducing after merging multiple bed,bim,fam files with Plink's --merge-list function


I have multiple BED/BIM/FAM files (from separate GWAS experiments) and I wish to create a merged set of these files.
I am using the command:

plink --bfile myfile1 --merge-list all_my_files.txt --make-bed --out mymerged

my_files.txt has the format:

file2.bed file2.bim file2.fam 
fileK.bed fileK.bim fileK.fam

The problem is I am merging the files for about 3000 samples (divided into about 34 GWAS runs). When I do a line count (wc -l ) for the resulting fam file from the merged exercise, I get about 2400. I want to know why is the information for almost 600 samples lost?





Source link