Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

          Latest Articles

          Collapse

          • seqadmin
            Current Approaches to Protein Sequencing
            by seqadmin


            Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
            04-04-2024, 04:25 PM
          • seqadmin
            Strategies for Sequencing Challenging Samples
            by seqadmin


            Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
            03-22-2024, 06:39 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 04-11-2024, 12:08 PM
          0 responses
          21 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-10-2024, 10:19 PM
          0 responses
          23 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-10-2024, 09:21 AM
          0 responses
          18 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-04-2024, 09:00 AM
          0 responses
          49 views
          0 likes
          Last Post seqadmin  
          Working...
          X