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?
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