Hi,

I have an lgen file that looks like this

FID    ID     SNP    allele1_AB     allele2_AB
Y     131   ARS-5       A                  A
Y     131   ARS-2       A                  B
Y     131   ARS-7       B                  B

From this I want to create a VCF file with the genotypes as 0/0, 0/1 and 1/1.

I am using plink --cow --file wagyu --recode vcf but I get a warning

Warning: At least one VCF allele code violates the official specification;
other tools may not accept the file.  (Valid codes must either start with a
'<', only contain characters in {A,C,G,T,N,a,c,g,t,n}, be an isolated '*', or
represent a breakend.)

How can I go about this without losing data. I can't use --snps-only just-acgt because I have alleles A and B.

Thanks.