I didn't want to make Annovar::Wrapper a part of the BioPerl distribution.

Great, you don't have to, but since annovar is somekindof bio related module ...

If you look on CPAN for Wrapper you'll find lots of existing namespaces with a bunch of related modules and then a ::Wrapper module

You should drop ::Wrapper from the module name, add it to the description

=head1 NAME

Annovar - wrapper for bin/annovar
[download]

There are no annovar things on cpan

There are bioinformatics, gene reated modules

There are things like BioX::CLPM - Perl Tools for Mass Spec Peptide Matching

Which don't appear to depend on Bio::Perl

I can't find guidlines about "...X::..." modules...

And I'm not sure about Bio::Perl guidelines regarding BioX, but maybe BioX is like DBIx, where you can drop DBI/Bio adjacent modules

So now for your consideration (with the caveats)

BioX::Annovar - wrapper for openbioinformatics.org/annovar/ - functional annotation of genetic variants from high-throughput sequencing data