Linkage disequilibrium from multi-sample vcf file

Question

[felipead66]

I have a multi-sample vcf file annotated with snpeff.

I want to calculate the linkage disequilibrium.

I have 2 questions:

1. I use vcftools, in particular ./vcftools --vcf input_vcf.vcf --geno-r2 --out output and it takes forever (it runs a week and keeps on). Is this OK?

2. Is it appropriate to use the multi-sample vcf or should i calculate the ld for each vcf/sample?