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