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Old 10-26-2012, 01:15 PM   #1
turnersd
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Location: Charlottesville, VA

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Posts: 112
Default Problem running ANNOVAR: no avsift table

I'm trying to run the ANNOVAR script summarize_annovar.pl, but I'm having trouble downloading the avsift table. As per the instructions, I'm using:

Code:
$ mkdir hg19
$ annotate_variation.pl -buildver hg19 -downdb avsift hg19

NOTICE: The --sift_threshold is set as 0.05 by default
NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done
NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/avsift.txt.gz ... Failed
WARNING: Some files cannot be downloaded, including http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/avsift.txt.gz
Which tells me that the avsift.txt.gz file doesn't exist. When looking at http://hgdownload.cse.ucsc.edu/golde...hg19/database/, there is no file that matches the pattern "sift".

Where can I find this data?
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Old 10-26-2012, 01:28 PM   #2
sheenams
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The following just worked for me (note, I have the previous version of Annovar)

$ annotate_variation.pl -buildver hg19 -downdb avsift ann_test/
NOTICE: The --sift_threshold is set as 0.05 by default
NOTICE: the --webfrom argument is set to 'annovar' automatically for -dbtype of 'avsift'
NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done
----------------------------UPDATE AVAILABLE------------------------------
--------------------------------------------------------------------------
WARNING: A new version of ANNOVAR (dated 2012-10-23) is available!
Download from http://www.openbioinformatics.org/annovar/
Changes made in the 2012-10-23 version:
* added -veresp argument to summarize_annovar.pl to suppert esp6500 data set
* added -aamatrixfile argument to print out amino acid substitution scores such as Gratham scores
* changed UCSC download from FTP to HTTP to help users with firewall settings
* fixed a problem handling genericdb file when chr prefix is present for chromosomes
* fixed a problem downloading index for gerp++gt2 files
* added variants_reduction.pl program
--------------------------------------------------------------------------
--------------------------------------------------------------------------
NOTICE: Downloading annotation database http://www.openbioinformatics.org/an..._avsift.txt.gz ... OK
NOTICE: Downloading annotation database http://www.openbioinformatics.org/an...ift.txt.idx.gz ... OK
NOTICE: Uncompressing downloaded files
NOTICE: Finished downloading annotation files for hg19 build version, with files saved at the 'ann_test' directory


Maybe try to download from the website listed in my output?
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Old 10-26-2012, 01:59 PM   #3
turnersd
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Location: Charlottesville, VA

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Looks like the new version tries to link to UCSC rather than openbioinformatics.org... I'll email Kai Wang about this.
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Old 11-29-2012, 08:22 AM   #4
ccabrera
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Location: UK

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I used the following command:
Code:
annotate_variation.pl -downdb -webfrom annovar -buildver hg19 avsift humandb/
http://www.openbioinformatics.org/an..._download.html
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Old 11-29-2012, 11:50 AM   #5
turnersd
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Quote:
Originally Posted by ccabrera View Post
I used the following command:
Code:
annotate_variation.pl -downdb -webfrom annovar -buildver hg19 avsift humandb/
http://www.openbioinformatics.org/an..._download.html
Yep, I missed the -webfrom argument. Thanks.
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