Question: PLINK2 recode ped flag issue
gravatar for emyli
3.3 years ago by
emyli10 wrote:


I am trying to covert .ped and .map files to a VCF file using plink2, as in the examples below:

plink2 --ped test.ped  --map --recode vcf --out testVCF
plink2 --file test --recode vcf --out testVCF

However, I am thrown the errors:

Error: Unrecognized flag ('--ped').
Error: Unrecognized flag ('--file').

Can anyone explain why this is?

I have been able to do the conversion using plink, however the REF alleles are incorrectly assigned (as is a well documented issue), and I do not have access to a reference file for the ~400K markers to define the reference alleles. I believe that plink2 is meant to have addressed this issue, and should correctly assign REF alleles.

Thanks in advance for any insight.

ped plink plink2 vcf • 1.9k views
ADD COMMENTlink modified 3.3 years ago by tarek.mohamed270 • written 3.3 years ago by emyli10
gravatar for tarek.mohamed
3.3 years ago by
tarek.mohamed270 wrote:

Hi emily,

Try this plink 1.9-beta-4.6

plink --ped test.ped --map --recode-vcf --out test_vcf
ADD COMMENTlink written 3.3 years ago by tarek.mohamed270

Thanks for the suggestion, I believe this is the version I have been using (binary download ofStable (beta 4.6, 15 Aug) for OS X (64-bit) from I tried again using your modified command and am getting the same result, I am using to assess the validity of the output vcf, and am told most of the sites have inconsistent reference alleles.

ADD REPLYlink written 3.3 years ago by emyli10

What do you mean by REF alleles are incorrectly assigned. Can you attach an example.


ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by tarek.mohamed270
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