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  • PLINK: bed to vcf conversion

    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,

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