Question: Recode to VCF with -a2-allele flag in PLINK
gravatar for emyli
17 months ago by
emyli0 wrote:

Hi there,

I generated a VCF using plink from .ped and .map files from a genotyping experiment as so:

plink --file test --recode vcf --out testVCF

As is well documented, this assigned the REF alleles in the output VCF to be the major allele observed in the data.

I am trying to recode to make the VCF assign the correct REF allele as so:

plink --vcf testVCF --a2-allele reference_alleles.txt --recode vcf --out testVCF_corrected

I am met with the error:

--a2-allele: 0 assignments made.

I have tried formatting the reference_alleles.txt as:


exm77264    G
exm77266    C
exm77274    T



G   exm77264
C   exm77266
T   exm77274

As well as specifiying:

--a2-allele reference_alleles.txt  1 2


--a2-allele reference_alleles.txt  1 2

Any advice would be greatly appreciated, thanks!

recode plink vcf • 1.5k views
ADD COMMENTlink modified 15 months ago by Biostar ♦♦ 20 • written 17 months ago by emyli0

Hmm, the only way you should get "0 assignments made" is if the variant IDs in reference_alleles.txt don't match those in What do the first lines of look like? Can you post the full .log file from a failing --a2-allele run?

ADD REPLYlink modified 17 months ago • written 17 months ago by chrchang5234.8k

yes, but since the vcf option is being used then the variant IDs should be assigned in the VCF file itself.

ADD REPLYlink written 9 months ago by asif.zubair0
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