it goes wrong on the very last line of the file

Between the 2 foreach blocks, add these 2 lines of code.

$pval{$prev_join} = $prev_pval/$i;
$fst{$prev_join} = $prev_fst/$i;
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There were alot of warnings about some of your variables not being initialized. To get rid of the warnings, I initialized them with values from the first line in the file. Posting some of that code here.

open INFILE, "<$infile" or die $!;
chomp(my @lines = <INFILE>);
close INFILE or die $!;

my ($chr, $prev_loc, $prev_pval, $prev_fst) = (split /\t/, $lines[0])[
+1,2,5,6];
my $prev_join = "$chr-$prev_loc";

my $i=1;
my %pval;
my %fst;

foreach (@lines[1 .. $#lines]){
    my ($name, $chr, $location, $gen, $dom, $pval, $fst) = split /\t/;
    my $join = "$chr-$location";

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

    else {
        $pval{$prev_join} = $prev_pval / $i;
        $fst{$prev_join} = $prev_fst / $i;
        $i = 1;
    } 
    
    $prev_loc = $location;
    $prev_pval = $pval;
    $prev_fst = $fst;
    $prev_join = $join;
}

$pval{$prev_join} = $prev_pval/$i;
$fst{$prev_join} = $prev_fst/$i;


foreach (@lines){
    my ($name, $chr, $location, $gen, $dom, $pval, $fst) = split /\t+/
+;
    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";
}
[download]

There are 2 different criteria about what you use to create a group to average. In your code, a group to average is determined by the code, if ($location == $prev_loc) .... But you are also joining the $chr and $location keys for the 2 different hashes here. I believe this leaves the door open for difficult to trace behaviors. It works without error with the sample data provided, but it could break down with an actual file.

Would you want a line like if ($join eq $prev_join)...?

Why join the chr location columns. Can the same location have different 'chr' columns? If not, there is no advantage to combining them like that. They could be more simply using the location for the 2 hashes here and the keys are simple to sort, the keys being 'location' alone - a floating point number.

I compared the join of (chr, location), to determine the end of a run instead of just location by itself.

#!/usr/bin/perl
use strict;
use warnings;
use List::Util qw/ sum /;

chomp(my $line = <DATA>);
my $prev_chr_loc = join "-", (split /\t/, $line)[1,2];

my @lines = $line;

while (my $line = <DATA>) {
    chomp $line;
    my $chr_loc = join "-", (split /\t/, $line)[1,2];
    
    if ($chr_loc eq $prev_chr_loc) {
        push @lines, $line;
    }
    else {
        print "$_\n" for compute_avg( @lines );
        @lines = $line;
    }
    $prev_chr_loc = $chr_loc;
}

print "$_\n" for compute_avg( @lines );

sub compute_avg {
    my @lines = @_;
    
    my $avg_col5 = sprintf "%.9f",
        sum(map {(split /\t/)[5]} @lines) / @lines;
            
    my $avg_col6 = sprintf "%.9f",
        sum(map {(split /\t/)[6]} @lines) / @lines;
        
    for (@lines) {
        my ($c5,$c6) = (split /\t/)[5,6];
        s/$c5\t$c6$/$avg_col5\t$avg_col6/;
    }
    return @lines;
}
[download]

Update: Redid substitution for closer spec.

well I've written something that almost does the job, except it goes wrong on the very last line of the file.

Did you at any point sit down with pencil and paper, and write out steps to solve this problem as human computer with pen and paper?