plink vcf

Question

[samuel]

Hi, I'm a complete newbie using plink. I have the .bat .map and .ped files. I have then produced a vcf file with

plink --file {prefix} --recode-vcf --out {prefix-out}

This creates a vcf like so:

1       357385       rs182004761     G       A       .       .       PR      GT      0/0     1/0     0/0     1/1

Is there a way of converting this so that instead of the genotypes being 0/0 etc they have the base IDS eg:

1       357385       rs182004761     G       A       .       .       PR      GT      G/G     G/A     G/G     A/A

Answer 1

[chrchang523]

What you’re asking for is not a VCF file. Either change your question to specify that you don’t want a VCF file, or delete the question.