I tried doing:
> library(vcfR) > vcf <- read.vcfR("ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf", verbose = FALSE )
but this takes forever to load and I am not sure it is even working.
Any other suggestion on how I can read in .vcf file in R?
I intend to create covariance matrix file from this data.