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  • 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?

  • #2
    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?

    Comment


    • #3
      Looks like the new version tries to link to UCSC rather than openbioinformatics.org... I'll email Kai Wang about this.

      Comment


      • #4
        I used the following command:
        Code:
        annotate_variation.pl -downdb -webfrom annovar -buildver hg19 avsift humandb/

        Comment


        • #5
          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.

          Comment

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