Question: PLINK: Unrecognized flag '--list-duplicate-vars'
gravatar for alesssia
5.2 years ago by
London, UK
alesssia560 wrote:

Hi All.

I'm trying to use BEAGLE4 to do an IBD analysis. My files are in PLINK format, thus I used PLINK (v1.9) to generate the VCF file (with the "--recode vcf" flag).  Unfortunately I have duplicated markers in the same position (as pointed out by a Beagle exception).

According to the PLINK documentation I could use the flag "--list-duplicate-vars" to identify and then remove them (with the flag --exclude), but when I run it PLINK with the following command:

       $ plink --file myfile --list-duplicate-vars ids-only 

it returns:

      Error: Unrecognized flag ('--list-duplicate-vars').

Does anyone has any suggestions? 

Thanks in advance for your help,


beagle plink ibd • 3.9k views
ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by alesssia560

Solved after a PLINK update. The flag was added on Dec 11th, 2014.

Thanks to Christopher Chang :)

ADD REPLYlink written 5.2 years ago by alesssia560
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