Question: downloading zebrafish snps for annovar
gravatar for mark.dunning
8 months ago by
The University of Sheffield
mark.dunning200 wrote:


I am hoping to use annovar to annotate some zebrafish genome coordinates, and would like to incorporate snp positions.

I can download reference sequences with the following tmp/danRer11_refGene.txt -seqdir tmp/danRer11_seq -format refGene -outfile tmp/danRer11_refGeneMrna.fa

Can anyone tell me the command I need to download an appropriate snp database for zebrafish? The following results in error -downdb snp129 -buildver danRer11 tmp


zebrafish annovar • 238 views
ADD COMMENTlink written 8 months ago by mark.dunning200

Have you tried -buildver danRer11 -downdb avdblist -webfrom annovar?

EDIT: Turns out that might not work for non-human organisms: A: List all available databases for ANNOVAR

ADD REPLYlink modified 8 months ago • written 8 months ago by RamRS21k
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