Question: Creating Binary file (*.bed, *.bim, *.fam file) from 1000GP LEGEND file
0
gravatar for tesfadej2003
2.1 years ago by
tesfadej200310
tesfadej200310 wrote:

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.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by tesfadej200310
2
gravatar for chrchang523
2.1 years ago by
chrchang5234.8k
United States
chrchang5234.8k wrote:

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).

ADD COMMENTlink written 2.1 years ago by chrchang5234.8k

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.

ADD REPLYlink written 2.1 years ago by tesfadej200310
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