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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downloaded the latest versions of the software and the databases but when I run it I get an error saying the index is out of date.

WARNING: Your index file annovar_latest/humandb/hg19_cadd.txt.idx is out of date and will not be used.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?

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Your safest bet is to just redownload the annotation. 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 with a single perl script that allegedly recreates the index.

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  • $\begingroup$ 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 I don't see how they could possibly be out of date because there is nothing in there other than row numbers. $\endgroup$
    – Greg
    Commented Aug 6, 2017 at 20:40
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    $\begingroup$ I downloaded everything again and it worked. Sometimes the simplest solution is the best. Thanks $\endgroup$
    – Greg
    Commented Aug 6, 2017 at 22:02

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