Creating Binary file (*.bed, *.bim, *.fam file) from 1000GP LEGEND file

Question

[tesfadej2003]

Hi All, I have the file "1000GP_Phase3_combined.legend".

I want to create a binary (*.bed, *.bim, *.fam file) PLINK file. Does anyone have experience?

Thank you in advance.

Answer 1

[chrchang523]

The .legend file is essentially PLINK's .bim, with a few extra columns. You also need .hap and .sample files to generate a full PLINK fileset (and you'll probably need to do some minor preprocessing on the 1000GP phase 3 .sample file to make it readable by existing tools).

[tesfadej2003]

Yes indeed, that minor preprocessing is probably using Perl program. However, I am not familiar with Perl. What a pity. I would be grateful if you would have the command line/script. Thank you so much for your time.