View Single Post
Old 04-21-2015, 12:01 PM   #1
Location: ca

Join Date: Nov 2014
Posts: 11
Default PLINK: bed to vcf conversion


This is really dumb! I looked at the FAQ/online etc., but couldn't find this....

I want to convert my files (xx.bed, xx.bim, xx.fam) to vcf format. I am following the code given at:

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: |
| |

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?

bsmith030465 is offline   Reply With Quote