ANNOVAR, 1000g database calling
That's a warning. Presumably, a match failed ($&amp; 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.