Hi,
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: http://pngu.mgh.harvard.edu/~purcell...ta.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?
thanks,
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: http://pngu.mgh.harvard.edu/~purcell...ta.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?
thanks,