plink vcf
1
0
Entering edit mode
3 months ago
zoegward ▴ 130

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
plink • 225 views
ADD COMMENT
0
Entering edit mode
3 months ago

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1477 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6