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  • VCF coodinates to Genomic Features from GFF

    I think this is a relatively simple question but I haven't been able to figure out a solution yet.

    Basically, I have a VCF file of variants and a GFF file of the genome with genomic features. I would like to extract the genomic features (introns, exons, etc.) of each of the variants in the VCF file.

    Is there a simple way to glean this information?

  • #2
    Have you tried using snpEff? I imagine that it can do most of what you want.

    Comment


    • #3
      Hmmm...have not seen snpEff before but it looks promising.

      Thanks for the pointer. I will give this a try.

      Any other solutions?

      Comment

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