Hi  all,

I am very new in this filed and really appriciate whoever can help me with this question. I was wondering if you how I can filter my bfiles( BIM, BED, FAM) for a subset of my SNPs. I have my BIM , BED, FAM files. But I do not need all SNPs available so I filterd my BIM file by AWK commands but I do not know how to match my BED file with the new BIM file created. Please  tell me how should I do it? thank you very much in advance.
you should create a list of your snps and use plink's filtering option.  I believe it goes something like :

    plink --bfile <yourfile> --remove [snps.txt] --out<newset>

this should also subset your BED file

