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  • Mapping SNPs to Chromosomes

    I have a reference genome (.fa) and its annotation (.gtf) files. I have sequenced both DNA and RNA from test sample and generated vcf files containing SNP and INDEL locations for each chromosome of the reference genome. I want to plot the identified SNPs and INDELs to identify hot spots on each chromosome. I have read about R being useful to do the same but was unable to narrow down on how to get it done. Please advise.......

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    To make it clear, I want to create image files of each chromosome indicating SNPs and INDELs at each location as provided in the vcf files.

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