Question: downloading zebrafish snps for annovar
0
gravatar for mark.dunning
8 weeks ago by
mark.dunning200
The University of Sheffield
mark.dunning200 wrote:

Hi,

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

retrieve_seq_from_fasta.pl 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

annotate_variation.pl -downdb snp129 -buildver danRer11 tmp

Thanks

zebrafish annovar • 127 views
ADD COMMENTlink written 8 weeks ago by mark.dunning200

Have you tried annotate_variation.pl -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 weeks ago • written 8 weeks ago by RamRS19k
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