The following solution is based on the version by mr_ron. The @keys array is for preserving key order. This is being posted mainly for demonstrating a version that is light on memory consumption.

#!/usr/bin/perl -an

use strict;
use warnings;

# usage: perl -an script.pl file.a file.b

our ( $db, @keys );

my $key = join "\t", @F[0 .. 3];

push @keys, $key unless exists $db->{ $key };

$db->{ $key }[0]++;
$db->{ $key }[1] += $F[4];
$db->{ $key }[2] += $F[5];

END {
   my ( $key, $aref, $cnt );

   while ( @keys ) {
      $key  = shift  @keys;
      $aref = delete $db->{ $key };

      ( ( $cnt = $aref->[0] ) > 1 )
         ? print $key."\t".( $aref->[1] / $cnt )."\t".$aref->[2]."\n"
         : print $key."\t".( $aref->[1]        )."\t".$aref->[2]."\n";
   }
}
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