well I've written something that almost does the job, except it goes wrong on the very last line of the file. I read the file into an array and calculate the averages which I then put into a hash and then iterate through the array and lookup values from the hashes. I'm sure there's a more elegant way to do it though....

#!/usr/bin/perl

# Usage: perl average_table.pl -i <input file>
use strict;
use warnings;
use Getopt::Long;
my $infile;
my @fields;
my @array;
my @values;
my %hash;
my $add_fst;
my @out;
my @count;
my $i=1;
my @final;
my %pval;
my %fst;

                my $prev_loc;
                my $prev_pval;
                my $prev_fst;
        my $prev_join;

GetOptions (
        "infile=s" => \$infile,
);


open INFILE, "<$infile" or die $!;
@fields = <INFILE>;
foreach (@fields){

        @array = split(/\t+/, $_);
        chomp (@array);
        my ($name, $chr, $location, $gen, $dom, $pval, $fst) = @array[
+0..6];
        my $join = "$chr-$location";
        push (@values, $join, $pval);

            if ($location == $prev_loc){
            $pval = $pval + $prev_pval;
            $fst = $fst + $prev_fst;
            $i++;
            }    

            elsif ($location != $prev_loc) { 
            my $pval_average = ($prev_pval / $i);
            my $fst_average = ($prev_fst / $i);
            my $join2 = "$prev_join\t$pval_average\t$fst_average";
            $pval{$prev_join} = $pval_average;
            $fst{$prev_join} = $fst_average;        
            push (@final, $join2);
            $i = 1;
            } 
        
        $prev_loc = $location;
        $prev_pval = $pval;
        $prev_fst = $fst;
        $prev_join = $join;
    }


foreach (@fields){
            @out = split(/\t+/, $_);
            chomp (@out);
            my ($name, $chr, $location, $gen, $dom, $pval, $fst) = @ou
+t[0..6];
                my $join = "$chr-$location";
        my $new_pval = $pval{$join};
        my $new_fst = $fst{$join};

        print $name."\t".$chr."\t".$location."\t".$gen."\t".$dom."\t".
+$new_pval."\t".$new_fst."\n";
        }
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