Linkage disequilibrium in unphased genotypic data

Question

[leslie.watson]

I have been trying to complete Linkage Disequilibrium on unphased genotypic data that there is no reference genome for. I have tried genepop,genepop web, snp analyzer, the LD option in Pegas (R), and arlequin, and Tassel. These programs are taking forever to run or the outputs dont seem to make sense. Does anyone have a solution to this problem?

[tiagoantao]

Can you give more information, namely: number of loci and individuals?

[su7880]

Hi,

Have you tried software "plink"? That worked fine with my data (SNPs from GBS without reference genome).

Answer 1

[Chris F.]

Why not just calculate it yourself? You could use Equation 2 from Storz and Kelly, for example, to get the between population component of LD. Depending on your goals, this might get you part or all of the way there.

Storz JF, Kelly JK (2008) Effects of spatially varying selection on nucleotide diversity and linkage disequilibrium: insights from deer mouse globin genes. Genetics 180:367–379. doi: 10.1534/genetics.108.088732