Question: Calculating LD between specific alleles even if they are not the minor alleles
gravatar for Vincent Laufer
2.0 years ago by
Vincent Laufer1.0k
United States
Vincent Laufer1.0k wrote:


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: 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.

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by Vincent Laufer1.0k

can't you recode the alleles manually and then run plink?

ADD REPLYlink written 2.0 years ago by stolarek.ir580
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 847 users visited in the last hour