I would like to know if it is possible to use SNPeff to predict SNPs effect impact on a species with no reference genome.
in the .vcf files that I'm currently working with there's a header line that provides information about the reference that was used. Maybe that can help you to find the reference (&download it) that was used to generate the .vcf that you want to annotate?
No, SnpEff requires a variant file and a reference genome that was used to build the variant file as input.
Thanks for your reply
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