Hi All Bioinformaticians,

I want to generate a 'LD heatmap' which depicts the decay in LD in the portions of genome where recombination has occured. For the same, I am using VCFtools to calculate LD. However, my doubt is, Does the script work for a haploid organism?

Is the '--hap-r2' argument in the script meant for Halpoid organism?

If not then how can I modify the script for haploid organism?

Thanks in advance

-Jigar