Question: List all available databases for ANNOVAR
3
gravatar for QVINTVS_FABIVS_MAXIMVS
2.8 years ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.2k wrote:

Several very commonly used annotation databases for human genomes are additionally provided below. In general, users can use -downdb -webfrom annovar in ANNOVAR directly to download these databases. To view of full list of databases (and their size and last changed date) prepared by ANNOVAR developers, use avdblist keyword in -downdb operation

Ok so I tried this

perl annotate_variation.pl -downdb avdblist

And this

perl annotate_variation.pl -downdb -webfrom annovar avdblist

And this

perl annotate_variation.pl -downdb -webfrom avdblist

And other variations and I get no list

WTF is it so hard to give an example of the exact command to use?

annovar • 4.0k views
ADD COMMENTlink modified 16 months ago by geocarvalho110 • written 2.8 years ago by QVINTVS_FABIVS_MAXIMVS2.2k
5
gravatar for QVINTVS_FABIVS_MAXIMVS
2.8 years ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.2k wrote:

Thanks to natasha.sernova I scrolled down a little bit and found the answer (and someone just as frustrated as me)

This works

$ perl annotate_variation.pl -webfrom annovar -downdb avdblist -buildver hg19 .

ANNOVAR needs better documentation

ADD COMMENTlink written 2.8 years ago by QVINTVS_FABIVS_MAXIMVS2.2k
2
gravatar for natasha.sernova
2.8 years ago by
natasha.sernova3.4k
natasha.sernova3.4k wrote:

http://annovar.openbioinformatics.org/en/latest/misc/faq/

• How to list all annotation databases in ANNOVAR web server?

“You can use -webfrom annovar -downdb avdblist to see a list of files, file sizes and time stamp. This only works on human genome though”.

But you have used a very close to this expression above but a little bit different one.

May be the difference is the reason of a problem...

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by natasha.sernova3.4k
1

Not an answer but this is what I get

$ perl annotate_variation.pl -webfrom annovar -downdb avdblist
Syntax error
ADD REPLYlink written 2.8 years ago by QVINTVS_FABIVS_MAXIMVS2.2k
1

Is your script supposed to work "with a list of files, file sizes and time stamp"?

If the script needs just a database, I would test it with a different one.

ADD REPLYlink written 2.8 years ago by natasha.sernova3.4k

I found the answer. Thanks to you!

ADD REPLYlink written 2.8 years ago by QVINTVS_FABIVS_MAXIMVS2.2k
1
gravatar for geocarvalho
16 months ago by
geocarvalho110
Brazil/Recife
geocarvalho110 wrote:

I had to use a directory to store the data

$ perl annotate_variation.pl -downdb -webfrom annovar avdblist humandb/ -buildver hg19

So you can open this file

$ more humandb/hg19_avdblist.txt
ADD COMMENTlink modified 16 months ago • written 16 months ago by geocarvalho110
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