List all available databases for ANNOVAR

Question

[QVINTVS_FABIVS_MAXIMVS]

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?

[Korsocius]

Hi, I have same problem:

perl annotate_variation.pl -webfrom annovar -downdb avdblist -buildver hg38 /home/fil/annovar/humandb/

NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg38_avdblist.txt.gz ... Failed WARNING: Some files cannot be downloaded, including http://www.openbioinformatics.org/annovar/download/hg38_avdblist.txt.gz is it possible that link is wrong in annotate_variation.pl?

Answer 1

[QVINTVS_FABIVS_MAXIMVS]

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 .

Answer 2

[geocarvalho]

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

Answer 3

[natasha.sernova]

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...

[QVINTVS_FABIVS_MAXIMVS]

Not an answer but this is what I get

$ perl annotate_variation.pl -webfrom annovar -downdb avdblist
Syntax error

[natasha.sernova]

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.

[QVINTVS_FABIVS_MAXIMVS]

I found the answer. Thanks to you!

[soyabean]

Just add <database-location> at the end of the code:

perl annotate_variation.pl -webfrom annovar -downdb avdblist -buildver hg38 humandb/

then you will get hg38_avdblist.txt in humandb/

Answer 4

[yuanma0427]

Here are the databases for hg38 you can download: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/

And for hg19: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/