Genotype frequencies Plink

Question

[Weavile]

Hi

I am fairly new to analyzing GWAS data using plink. I think I am getting the hang of it and really like plink as software. What I want to do is look at the frequencies of 2 SNPs occurring together between cases and controls.

For example

                      Frequency
rs101 A/T  rs202 C/G  Cases      Controls
A          C          ?          ?
A          G          ?          ?
T          C          ?          ?
T          G          ?          ?

e.g., I would like to know the percentage of Cases that had the combination of A & C ( for rs101 & rs202 respectively) using plink.

I hope that makes sense and any help would be appreciated.

Thanks in advance
Hank

Answer 1

[chrchang523]

--twolocus rs101 rs202 should do what you want.

[Weavile]

Exactly what I was looking for. Thanks a lot