Question: Annovar for mouse buildver and downdb?
2
gravatar for Sharon
2.8 years ago by
Sharon490
Sharon490 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 • 1.7k views
ADD COMMENTlink modified 7 months ago by v.chimankar0 • written 2.8 years ago by Sharon490
1

I am not sure that dbnsfp30a has data for mouse.

ADD REPLYlink modified 22 months ago • written 22 months ago by Kevin Blighe69k

Yes, I realised that also. Thanks Kevin :)

ADD REPLYlink written 21 months ago by Sharon490
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 21 months ago by Kevin Blighe69k

Hi there, I though you guys can help me out as you had similar issue. 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.

Thank you so much

ADD REPLYlink written 7 months ago by v.chimankar0

It sounds like you will have to download the data manually. First, try to see how ANNOVAR actually functions for, e.g., hg19 - then, you will realise that one can use any file for annotation.

ADD REPLYlink written 7 months ago by Kevin Blighe69k

Actually, you may want the retrieve_seq_from_fasta.pl function that comes with ANNOVAR - please take a look. Either way, ANNOVAR functions in a very logical fashion when it both builds DBs and annotates data. If you take some time to see how it functions, it will open up your world to be able to annotate anything with anything.

ADD REPLYlink modified 7 months ago • written 7 months ago by Kevin Blighe69k
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