PLINK: Convert bed,bim, fam to vcf file
2
1
Entering edit mode
8.4 years ago
bsmith030465 ▴ 230

Hi,

I want to convert my files (xx.bed, xx.bim, xx.fam) to vcf format. I am following the code given at: http://pngu.mgh.harvard.edu/~purcell/plink2/data.html#recode

Here is my command line output:

============================
node00:[exomes] % ls
exomes.bed exomes.bim exomes.fam

node00:[exomes] % plink --bfile exomes --recode vcf-iid --out ./new_vcf

@----------------------------------------------------------@
| PLINK! | v1.07 | 10/Aug/2009 |
|----------------------------------------------------------|
| (C) 2009 Shaun Purcell, GNU General Public License, v2 |
|----------------------------------------------------------|
| For documentation, citation & bug-report instructions: |
| http://pngu.mgh.harvard.edu/purcell/plink/ |
@----------------------------------------------------------@

Web-based version check ( --noweb to skip )
Recent cached web-check found...Problem connecting to web

Writing this text to log file [ ./new_vcf.log ]
Analysis started: Tue Apr 21 15:02:41 2015

** Unused command line option: vcf-iid

ERROR: Problem parsing the command line arguments.
==========================================

I also tried giving the options 'vcf' and 'vcf-fid' but got the same results.

What am I doing wrong? Or is there any other tool that I can use to achieve this?

Thanks

VCF PLINK RECODE BED • 9.7k views
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0
Entering edit mode

d'oh. Thanks!!

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3
Entering edit mode
8.4 years ago

You are using PLINK 1.07, and this command requires PLINK 1.9.

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0
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Where can I download 1.9? I only see download for latest stable and 'master', not 1.9 beta.

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Entering edit mode
8.2 years ago
Dan ▴ 520

deleted deleted

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