SNPeff method-no reference genome

Question

[Barby]

Hi there,

I would like to know if it is possible to use SNPeff to predict SNPs effect impact on a species with no reference genome.

Thanks B.R.

[Marvin]

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?

Answer 1

[aswathyseb]

Hi,

No, SnpEff requires a variant file and a reference genome that was used to build the variant file as input.

Answer 2

[Barby]

Thanks for your reply

BR