I have a multi-sample vcf file annotated with snpeff.
I want to calculate the linkage disequilibrium.
I have 2 questions:
I use vcftools, in particular
./vcftools --vcf input_vcf.vcf --geno-r2 --out outputand it takes forever (it runs a week and keeps on). Is this OK?
Is it appropriate to use the multi-sample vcf or should i calculate the ld for each vcf/sample?