SNP absolute number or density between chromosomes
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2.8 years ago
misterie ▴ 100

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

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