Very very very similar question Re: Help with locating bp region in chromosome/Re^5: Help with locating bp region in chromosome.

You might write as

#!/usr/bin/perl --
use strict; use warnings;
use autodie;
use Getopt::Long qw/ GetOptionsFromArray /;
use Pod::Usage;
use Regex::PreSuf ();

Main( @ARGV );
exit( 0 );

sub Main {    
    GetOptionsFromArray(
        \@_,
        'list=s'        => \my $inlist,
        'pos=s'        => \my $inpos,
        'out=s'        => \my $outpos,
        help            => sub { pod2usage(-verbose => 2); },
    ) or return pod2usage(2);
    return pod2usage(2) unless $inlist and $inpos and $outpos;
    
    my $list_re ;
    {
        open my($listfh), '<', $inlist;
        $list_re = Regex::PreSuf::presuf( map { chomp; $_ } readline( 
+$listfh ) );
        close $listfh;
    }
    open my($posfh), '<', $inpos;
    open my($outfh), '>', $outpos;
    while( <$posfh> ){
        my( $geneId, $SNPpos ) = ( split /\t/, $_ )[ 0, 2];
        if( $geneId =~ /$list_re/ ){
            print $outfh join "\t", $geneId, $SNPpos, "\n";
        }
    }
    close $posfh;
    close $outfh;
}

=head1 NAME

HI - hi

=head1 SYNOPSIS

    shaba -l foo.txt -p pos.txt -o out.txt
    shaba -l=foo.txt -p=pos.txt -o=out.txt
    shaba --help

=head1 ARGUMENS

=over 4

=item C<-list>

-list

=item C<-pos>

-pos

=item C<-out>

-out

=back

=cut
[download]

See also Tutorials: Variable Scoping in Perl: the basics, Coping with Scoping )

Also, Use Getopt::Long even if you don't think you need to - Mechanix