How to make bed file for existing bim and fam file

Question

[Mazza]

Hi every one. I had 22 different sets of bfiles each for each chromosome. I needed to aggregate them so I sued "cat" command for all .bim files and I created the aggregated .bim file. Then just use one of the .fam files since all of them are the same. But I do not know how to create the .bed file from the .fam and .bim file that I have since to create raw data I need them all.

Please help me with this since I really am in problem.

Answer 1

[Maxime Lamontagne]

Use plink with the --merge-list option.

plink --bfile Input-chr1 --merge-list List.txt --make-bed --out New-Output

List.txt :

Input-chr2.bed Input-chr2.bim Input-chr2.fam

Input-chr3.bed Input-chr3.bim Input-chr3.fam

...