Answers.Body: <p>Your safest bet is to just <a href="http://annovar.openbioinformatics.org/en/latest/user-guide/download/#additional-databases" rel="nofollow noreferrer">redownload the annotation</a>. I've not seen official documentation of the index used by annovar, but apparently it's just a text file with a single line header and chromosome-bin coordinates. Over on SEQanswers, <a href="http://seqanswers.com/forums/showthread.php?t=23535" rel="nofollow noreferrer">there's a thread discussing this issue</a> with a single <a href="http://seqanswers.com/forums/attachment.php?attachmentid=3818&amp;d=1432814490" rel="nofollow noreferrer">perl script</a> that allegedly recreates the index.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-08-06T20:40:54.300Z
Answers.Text: I just downloaded them again this morning, so that doesn't seem to work.  I have a job running the perl script fro that post to generate new index files.  If that works I'll report back.
  
  I don't see how they could possibly be out of date because there is nothing in there other than row numbers.
Answers.UserDisplayName: Greg
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-08-06T22:02:27.390Z
Answers.Text: I downloaded everything again and it worked.  Sometimes the simplest solution is the best.  Thanks
Answers.UserDisplayName: Greg
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-08-06T20:36:58.513Z
Answers.LastActivityDate: 2017-08-06T20:36:58.513Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I'm trying to use Annovar to annotate some variants with their CADD and FATHMM scores. I've downloaded the latest versions of the software and the databases but when I run it I get an error saying the index is out of date.</p>
  
  <blockquote>
    <p>WARNING: Your index file annovar_latest/humandb/hg19_cadd.txt.idx is out of date and will not be used. ANNOVAR can still generate correct results without index file.</p>
  </blockquote>
  
  <p>It still runs without the index file but it is extremely slow. How can I update the index file?</p>
  
Tags: <sequence-annotation>
Title: Annovar index out of date
ThreadText: # Annovar index out of date
  
  (Asked by: username_0 on 2017-08-06)
  
  I'm trying to use Annovar to annotate some variants with their CADD and FATHMM scores. I've downloaded the latest versions of the software and the databases but when I run it I get an error saying the index is out of date.
  
  > WARNING: Your index file annovar\_latest/humandb/hg19\_cadd.txt.idx is out of date and will not be used. ANNOVAR can still generate correct results without index file.
  
  It still runs without the index file but it is extremely slow. How can I update the index file?
  
  **Tags:** sequence-annotation
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-08-06. Score: 2 | Accepted answer
  
  Your safest bet is to just [redownload the annotation](http://annovar.openbioinformatics.org/en/latest/user-guide/download/#additional-databases). I've not seen official documentation of the index used by annovar, but apparently it's just a text file with a single line header and chromosome-bin coordinates. Over on SEQanswers, [there's a thread discussing this issue](http://seqanswers.com/forums/showthread.php?t=23535) with a single [perl script](http://seqanswers.com/forums/attachment.php?attachmentid=3818&d=1432814490) that allegedly recreates the index.
  
  > **Comments:**
  > **username_0**: I just downloaded them again this morning, so that doesn't seem to work.  I have a job running the perl script fro that post to generate new index files.  If that works I'll report back.  I don't see how they could possibly be out of date because there is nothing in there other than row numbers.  
  > **username_0**: I downloaded everything again and it worked.  Sometimes the simplest solution is the best.  Thanks  
  
  ---
  
  