Here's a way to get a text file containing counts of variants per 1Mb bin across hg38 (replace with your assembly of choice):

$ fetchChromSizes hg38 \
    | awk -vOFS="\t" '{ print $1, "0", $2; } \
    | grep -vE '*_*' \
    | sort-bed - \
    | bedops --chop 1000000 - \
    | bedmap --echo --count --delim '\t' - <(vcf2bed < variants.vcf) \
    > answer.txt

Once you have answer.txt, you can bring that into R to make a density plot with ggplot2.

I have an example Rscript from a previous question, which demonstrates use of geom_tile for making an ideogram-like figure similar to what is in your question:

Plotting SNP density heatmap chromosome ideogram