Question: Annovar for mouse buildver and downdb?
2
gravatar for Sharon
16 months ago by
Sharon440
Sharon440 wrote:

Hi All

I am trying to use annovar for mosue data. I used this command to create the mouseDB:

perl annotate_variation.pl -buildver mm10 -downdb -webfrom annovar refGene mousedb/

And it works fine and got he refgene db for mouse.

Now, I need to build the rest of annotation fields. something like humanDB: Something like this work on human but doesn't in mouse:

perl annotate_variation.pl -buildver mm10 -downdb -webfrom annovar dbnsfp30a mousedb/

Anyone knows the corresponding way for getting annotations for mouse?

Thanks

annovar vcf • 660 views
ADD COMMENTlink written 16 months ago by Sharon440
1

I am not sure that dbnsfp30a has data for mouse.

ADD REPLYlink modified 4 months ago • written 4 months ago by Kevin Blighe46k

Yes, I realised that also. Thanks Kevin :)

ADD REPLYlink written 3 months ago by Sharon440
1

Well, judging by their manuscript, they should have something for mouse in dbNSFP v3.0 ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4752381/ ) - it could just be that it is not yet implemented in ANNOVAR.

ADD REPLYlink written 3 months ago by Kevin Blighe46k
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