How to match alleles for a pair of SNPs using PLINK?

Question

[Tao]

Hi,

I have a list of variants which are in high LD of a list of GWAS variants. Basically, I want to know the likely risk alleles for proxy variants of a GWAS SNP. For example, we have two SNPs: rsA (A/C) and rsB (T/G), how can I infer the the matching alleles (the most likely haplotype). I would prefer using Plink and based on 1000G EUR genotyping data. And my input file would be two columns of variants to be matched.

I understand that LDlink server can do the allele pairing online or using URLs in a certain format. But, it's not so flexible. I have a feeling that Plink can do this, but anyone know how? Thanks!

Tao

Answer 1

[Tao]

In pairwise LD calculation of a given SNP pairs, Plink will output the corresponding haplotypes, see the example here. But it also need to be calculated one pair by one pair. And following scripts would be needed to satisfy my need.