Question: Annovar for mouse buildver and downdb?
2
gravatar for Sharon
23 months ago by
Sharon460
Sharon460 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 • 1.0k views
ADD COMMENTlink written 23 months ago by Sharon460
1

I am not sure that dbnsfp30a has data for mouse.

ADD REPLYlink modified 12 months ago • written 12 months ago by Kevin Blighe56k

Yes, I realised that also. Thanks Kevin :)

ADD REPLYlink written 11 months ago by Sharon460
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 11 months ago by Kevin Blighe56k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1142 users visited in the last hour