I have a list of SNPs across several populations. Because I am dealing with transethnic data, it frequently happens that the minor allele in one population is the major allele in another, so this distinction loses a bit of meaning.
As such, I computed Z-statistics on one specific allele of the data regardless of whether that allele is major or minor, and standardized this across all populations. I am calling the allele tested the effect allele and the other one the alternate allele.
I would now like to compute LD between only the effect alleles. I was reading the plink documentation here: http://zzz.bwh.harvard.edu/plink/ld.shtml#ld2 but it seems like plink automatically uses the "1" allele as the minor allele even if that isn't the reference allele in my data. So I was searching for a tool that will allow me to generate a NxN LD matrix between effect alleles easily. I have the data in plink .bed .bim .fam format right now, but I could convert it if necessary. Thanks.