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Question: SNPeff method-no reference genome
0
gravatar for Barby
9 months ago by
Barby • 20
Barby • 20 wrote:

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.

snp next-gen genome • 286 views
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modified 9 months ago • written 9 months ago by Barby • 20

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?

ADD REPLY • link written 9 months ago by Marvin • 90
1
gravatar for aswathyseb
9 months ago by
aswathyseb • 30
aswathyseb • 30 wrote:

Hi,

No, SnpEff requires a variant file and a reference genome that was used to build the variant file as input.
ADD COMMENT • link written 9 months ago by aswathyseb • 30
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gravatar for Barby
9 months ago by
Barby • 20
Barby • 20 wrote:

Thanks for your reply

BR
ADD COMMENT • link written 9 months ago by Barby • 20
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