Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • bsmith030465
    Member
    • Nov 2014
    • 13

    #1

    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,

Latest Articles

Collapse

  • SEQadmin2
    Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
    by SEQadmin2



    Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

    Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating
    ...
    10-14-2026, 09:55 AM
  • SEQadmin2
    New Genomics Technologies Take Aim at Long-Standing Limits
    by SEQadmin2


    Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

    We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing
    ...
    09-28-2026, 10:25 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, Yesterday, 11:13 AM
0 responses
16 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, Yesterday, 10:48 AM
0 responses
16 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-15-2026, 10:52 AM
0 responses
35 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-14-2026, 05:39 AM
0 responses
42 views
0 reactions
Last Post SEQadmin2  
Working...