I have recently downloaded Annovar, and succesfully filtered my files with a few databases, downloaded from Annovar. But when I try to do the exact same thing with the 1000 genomes project database, I get this error many times in the terminal, one for each line of **.

Argument "&" isn't numeric in numeric eq (==) at annotate_variation.pl line 1962, <DB> line &&.

& can be A, C, G, or T.

&& every line of the database

I have tried filtering with 1000g, 1000g2010 and 1000g2010jul databases, but all give these errors.

An example of the commands I use for filtering:

perl annotate_variation.pl --filter --dbtype CEU.sites.2010_07 testfile1.txt humandb/

Can anyone tell me if I'm doing something wrong, if this is known, and if I can do anything about it?

  • $\begingroup$ Is it an error (i.e. it stops the script from proceeding further) or a warning (i.e. alerts you with a message but doesn't stop execution)? IIRC this is a common warning with most ANNOVAR operations. $\endgroup$ – Ram RS May 30 '19 at 13:44

That's a warning. Presumably, a match failed ($& is the default Perl variable which holds the result of a match operation). So something in your input is not exactly what the script was expecting. You can probably safely ignore these messages.

Alternatively, update your question and add a few example lines of input which we can use to reproduce the error and maybe we can figure something out. If that isn't possible, at least show us line 1962 of the annotate_variation.pl script since that's the one that's failing.

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