I would like to calculate LD statistics for a VCF file using VCFtools. For the 1Mb window I am interested in, even using a R^2 minimum of 0.2, it is taking quite a bit of time to calculate these statistics.

I am ultimately only interested in LD statistics that include a single SNP of interest. Is there a way to have VCFtools compute LD stats only for pair-wise comparisons that include my SNP of interest, but still over the whole 1Mb region?

My understanding is that the "ld-window" options can define only the entire region to use, so they are not useful for this application.

That's useful, and means the conversion to plink is now unnecessary, cheers.