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SNP absolute number or density between chromosomes

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: enter image description here

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

snp annotated density
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updated by pltbiotech_tkarthi pltbiotech_tkarthi • written by misterie misterie

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

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written by pltbiotech_tkarthi pltbiotech_tkarthi

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