I am performing a K-mer based GWAS on my dataset. I have obtained some k-mers that are significantly associated with the trait of interest. Now, I want to perform a linkage disequilibrium (LD) analysis among those significant K-mers and create a heatmap as it is done with SNPs. But the problem is that the positioning of the k-mers is not know as it is a reference-free method. I have a table with presence/absence pattern of the associated k-mers in my samples.
Does someone have any idea how can I measure the LD among the significant k-mers?
I have the Plink binary files (*.bim, *.bed and *.fam files) containing the K-mer data that I used for GWAS.
Please let me know if you have any ideas.