johngg@shiraz:~/perl/Monks > perl -Mstrict -Mwarnings -E '
open my $inFH, q{<}, \ <<EOD or die $!;
ID   Type Pos
1    1    10
2    1    11
3    1    11
4    1    15
5    2    5
6    2    5
7    2    7
EOD

my $hdrs = <$inFH>;
my %tp;

foreach ( <$inFH> )
{
    my $key = sprintf q{%09d:%09d}, ( split )[ 1, 2 ];
    push @{ $tp{ $key } }, $_;
}

my @dupKeys =
   sort
   grep { scalar @{ $tp{ $_ } } > 1 }
   keys %tp;

print @{ $tp{ $_ } } for @dupKeys;'
2    1    11
3    1    11
5    2    5
6    2    5
johngg@shiraz:~/perl/Monks >