PLINK2 recode ped flag issue

Question

[emyli]

Hi,

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 .test.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.

Answer 1

[tarek.mohamed]

Hi emily,

Try this plink 1.9-beta-4.6

plink --ped test.ped --map test.map --recode-vcf --out test_vcf

[emyli]

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 https://www.cog-genomics.org/plink2). I tried again using your modified command and am getting the same result, I am using checkVCF.py to assess the validity of the output vcf, and am told most of the sites have inconsistent reference alleles.

[tarek.mohamed]

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

T