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  • filtering variants to just those in CDS

    I am trying to filter a vcf file of variants down to just those that reside within exons. I'm working with the malaria parasite Plasmodium falciparum.

    Is there a software you'd recommend for this purpose?

    Most of the ones I've found seem to be designed almost exclusively for use with human data. I tried working with SNPEff, but I can only get it to annotate everything. I can't seem to get it to filter out variants I'm not interested in.

  • #2
    SnpSift is the partner tool to SnpEff for filtering variants.

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