SNP absolute number or density between chromosomes

Question

[misterie]

Hi,

I have VCF file with annotation of SNP for each chromosome. I would like to compare numbers (proportion) of different type of variants (intergenic, exonic, UTR etc.) between each chromosomes. I calculated percent of e.g. intron, exon in each chromosome:

But it is just a percentages... It does not account the different length of chromosomes and other features. How can I better compare number of intergenic variants taking account of other features? Or other method?

Thank you in advance

[pltbiotech_tkarthi]

Did you try Variant Effect Predictor server at ENSEMBL using your VCF file?