Try this out: https://github.com/pwwang/vcfstats

I wrote http://lindenb.github.io/jvarkit/VcfStatsJfx.html

quickly wrote a java FX app displaying basic VCF stats : https://t.co/CxURRnKMre pic.twitter.com/chmS9ciuv9

— Pierre Lindenbaum (@yokofakun) April 9, 2018

Another option: https://vcf.iobio.io

Take a look at this: plot-VCF

It allows you to plot different VCF localization and gene analysis straight from your VCF file

As example, you can directly plot the mutation rate (overall, grouped and single-sample) for each gene:

Or plot variants based on any of their flags in VCF (e.g. Variant Allele Frequency):

And many more options (well documented on the GitHub page)