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:

A)

exm77264    G
exm77266    C
exm77274    T

and

B)

G   exm77264
C   exm77266
T   exm77274

As well as specifiying:

--a2-allele reference_alleles.txt  1 2

or

--a2-allele reference_alleles.txt  1 2

Any advice would be greatly appreciated, thanks!