Annovar: Mouse database download
Entering edit mode
4.1 years ago

Hi there,

I want to work with specific mouse strain from ucsc browser (A/J) on my annovar. How do I download it? perl -buildver mm10 -downdb -webfrom annovar refGene mousedb --> is for mm10 db I have tried --> perl -buildver 16 Strains -downdb -webfrom annovar refGene mousedb. I have tried different combination of words to replace mm10 with strains but it's not working.

annovar mouse database ucsc aj strain • 1.7k views
Entering edit mode
2.8 years ago
Luis Nassar ▴ 660


I'm not all that familiar with annovar, but I believe it requires UCSC databases to run. The mouse strains are actually assembly hubs ( You can see more info on them here (

For example, looking at your commands these hubs do not have a refGene track. You would have to use alternative gene annotations (we offer Ensembl and Augustus). You may be able to replicate this by download the data. You can find the A_J strain assembly files here:

And the annotations, including gene predictions, here:

Contacting annovar directly may be your best bet, but if you have any additional questions regarding UCSC or its data, our public help desk can always be reached at You may also send questions to if they contain sensitive data. For any Genome Browser questions on Biostars, the UCSC tag is the best way to ensure visibility by the team.


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