I'm trying to calculate LD between loci on different chromosomes using plink on the 1000 genomes vcf data. I plan on following this thread to convert my vcf files to bed and then merge all chromosomes into a single file: https://groups.google.com/forum/#!topic/plink2-users/RNztDLWCfB8 Then I plan on simply using the plink implementation from here to calculate LD: https://www.cog-genomics.org/plink/1.9/ld

Is there a simpler way to do this? Am I disregarding anything or doing something wrong?