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!