Annovar: Mouse database download

Question

[v.chimankar]

Hi there,

I want to work with specific mouse strain from ucsc browser (A/J) on my annovar. How do I download it? perl annotate_variation.pl -buildver mm10 -downdb -webfrom annovar refGene mousedb --> is for mm10 db I have tried --> perl annotate_variation.pl -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.

Answer 1

[Luis Nassar]

Hello,

I'm not all that familiar with annovar, but I believe it requires UCSC databases to run. The mouse strains are actually assembly hubs (https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html). You can see more info on them here (https://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hubIndex.html).

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:

http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/GCA_001624215.1_A_J_v1/

And the annotations, including gene predictions, here:

http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/GCA_001624215.1_A_J_v1/bbi/

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 [e-mail]. You may also send questions to [e-mail] 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.