Question: SNPeff method-no reference genome
0
gravatar for Barby
9 months ago by
Barby20
Barby20 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
ADD COMMENTlink modified 9 months ago • written 9 months ago by Barby20

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 REPLYlink written 9 months ago by Marvin90
1
gravatar for aswathyseb
9 months ago by
aswathyseb30
aswathyseb30 wrote:

Hi,

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

ADD COMMENTlink written 9 months ago by aswathyseb30
0
gravatar for Barby
9 months ago by
Barby20
Barby20 wrote:

Thanks for your reply

BR

ADD COMMENTlink written 9 months ago by Barby20
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