ANNOVAR annotation error

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Hi, I am getting the following error message when I am trying to run ANNOVAR annotation on a vcf file in order to identify genes with polymorphic sites;
WARNING to old ANNOVAR users: this program no longer does line-to-line conversion for multi-sample VCF files. If you want to include all variants in output, use ‘-format vcf4old’ instead.
NOTICE: Finished reading 2339 lines from VCF file
NOTICE: A total…

Can anyone please help me on this?

1 Like
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Welcome, @umagaur

More information about the error is needed to help troubleshoot.

Where how/to find this:

Other info that will help:

  1. Where are you working? URL if public server, or describe if otherwise.
  2. What version of Annovar are you using? Please post back the entire tool name/version found at the top of the tool form. (Click on the “double circle” icon to bring back up the original job form).
  3. Some public servers have a few built-in Annovar indexes and some have none. Your own server may be customized. Or you may be providing annotation inputs on the tool form. Please explain a bit about your case and include the genome build (“database”) assigned to the VCF and other inputs (if provided separately).
  4. How was the input VCF created? Or did you source it from somewhere? Please briefly explain.
  5. If you are following a tutorial or a tutorial’s associated workflow, please share the link and note the step you are at, plus if you are using the tutorial data or your own.

More could be going on but let’s start there. Thanks!