If your motive is to see if any variant in the VCF is within repeats, then you could do something like this -
1) Get the BED format file of repeats in our organism of interest
2) Then use bedtools coverage (here) to see overlap with repeats.
This relies on availability of repeat strt end pos. in your organism of interest. For many org., you can get such BED from UCSC Table Browser like this -
(Use Clade and Genome pull down menu to arrive at other organisms)