S1 File. The in-house PERL scripts.
#!perl
use warnings;
use strict;
use Getopt::Long;

my %opts;
GetOptions(\%opts, "i=s", "f=s", "p=s", "o=s", "w=i", "s=i");

my $usage = <<"USAGE";
	Usage:  perl $0 -i <file> -f <fa.fai> -p <population(A=number 1,B=number 2)> -o <outprefix> -w [window]
	!!! set '-' for missing genotype !!!
	Options:
		-i       file        input file
		-f       file        input fai of fasta
		-p       string      2 population, sort by header of file, eg: A=10,B=15; A is blank, B is treat
		-o       string      outprefix
		-w       int         slide window, default 50000
USAGE

die $usage if(!$opts{i} or !$opts{f} or !$opts{p} or !$opts{o});

$opts{w} ||= 50000;
my $s = $opts{w} / 2;

my (@id, @nsample, $allsample);
my @popu = split /,/, $opts{p};
foreach(@popu)
{
	my ($x, $y) = (split /=/);
	push @id, $x;
	$allsample += $y;
	push @nsample, $y;
}
die "Just only calculate 2 population!\n" if(@id != 2);
my @pid = map {$_ .= "_pi"} @id;
my @oid = map {$_ =~ s/_pi//;$_ .= "_omega"} @id;
my @tid = map {$_ =~ s/_omega//;$_ .= "_tajiamaD"} @id;
my @hid = map {$_ =~ s/_tajiamaD//;$_ .= "_Hp"} @id;
my $rid = "$pid[1]/$pid[0]";
open OO, "> $opts{o}.omegapi.txt" or die $!;
print OO join("\t", "#chr\tloci", @oid, @pid, $rid, "all_pi", "Fst", @tid, @hid)."\n";

my (@tmp, %chr);
open FA, $opts{f} or die $!;
while(<FA>)
{
	chomp;
	@tmp = split;
	$chr{$tmp[0]} = $tmp[1];
}
close FA;

my %hash;
open FB, $opts{i} =~ /\.gz$/ ? "gzip -dc $opts{i} |" : $opts{i} or die $!;
<FB>;
while(<FB>)
{
	chomp;
	@tmp = split;
	push @{$hash{$tmp[0]}}, join("\t", $tmp[1], @tmp[2..$#tmp]);
}
close FB;

foreach(sort {$a cmp $b} keys %chr)
{
	next unless(exists $hash{$_});
	my $n = int($chr{$_} / $s);
	for(my $i = 0; $i <= $n; $i ++)
	{
		my $start = $s * $i + 1;
		my $end = $opts{w} + $s * $i;
		my $nloci = 0;
		my @lines;
		for(my $j = 0; $j < @{$hash{$_}}; $j ++)
		{
			my @line = split /\t/, $hash{$_}[$j];
			if($line[0] >= $start and $line[0] <= $end)
			{
				$nloci ++;
				push @lines, join("\t", @line[1..$#line]);
			}elsif($line[0] > $end){
				last;
			}
			# delete locis of last step
			if($line[0] >= $start and $line[0] <= (($i+1) * $s))
			{
				shift @{$hash{$_}};
				$j -= 1;
			}
		}
		my $rawlen = int(($start + $end) / 2);
        if($nloci == 0)
        {
            my @zero = (0) x 11;
            print OO join("\t", "$_\t$rawlen", @zero)."\n";
            next;
        }
		
		my (@aomega, @bomega, @api, @bpi, @allpi, @avepi, @piratio, @fst, @ahp, @bhp, @atajimad, @btajimad);
		foreach my $l(@lines)
		{
			my @ls = split /\t/, $l;
			my $REF = shift @ls;
			my ($aref, $ahet, $amut, $bref, $bhet, $bmut) = (0) x 6;
			for(my $k = 0; $k < $nsample[0]; $k ++)
			{
				if($ls[$k] eq $REF)
				{
					$aref ++;
				}elsif($ls[$k] =~ /[ATCG]/){
					$amut ++;
				}elsif($ls[$k] ne "-"){
					$ahet ++;
				}
			}
			for(my $k = $nsample[0]; $k < $allsample; $k ++)
			{
				if($ls[$k] eq $REF)
				{
					$bref ++;
				}elsif($ls[$k] =~ /[ATCG]/){
					$bmut ++;
				}elsif($ls[$k] ne "-"){
					$bhet ++;
				}
			}
			my $aeffectsample = $aref + $amut + $ahet;
			my $beffectsample = $bref + $bmut + $bhet;
			
			# calculate Omega
			my $aomega_v = 1 / 1 / &tt($aeffectsample);
			my $bomega_v = 1 / 1 / &tt($beffectsample);
			push @aomega, $aomega_v;
			push @bomega, $bomega_v;

			# calculate Pi
			my $api_v = $aeffectsample >= 2 ? (0.5 * ($aref * $ahet + $amut * $ahet) + $aref * $amut) / ($aeffectsample * ($aeffectsample - 1) / 2) : 0;
			my $bpi_v = $beffectsample >= 2 ? (0.5 * ($bref * $bhet + $bmut * $bhet) + $bref * $bmut) / ($beffectsample * ($beffectsample - 1) / 2) : 0;
			push @api, $api_v;
			push @bpi, $bpi_v;
			my $allpi_v = (0.5 * ($aref * $bhet + $bref * $ahet + $amut * $bhet + $bmut * $ahet) + $aref * $bmut + $bref * $amut) / ($aeffectsample * $beffectsample);
			push @allpi, $allpi_v;
			push @avepi, ($api_v + $bpi_v) / 2;
            #push @piratio, $api_v == 0 ? 0 : $bpi_v / $api_v;
			
			# calculate fst
            #my $fst_v = 1 - ($api_v + $bpi_v) / 2 / $allpi_v;
            #push @fst, $fst_v;
			
			#calculate tajimad
			push @atajimad, $aeffectsample <= 3 ? 0 : ($api_v - $aomega_v) / &sdd($aeffectsample);
			push @btajimad, $beffectsample <= 3 ? 0 : ($bpi_v - $bomega_v) / &sdd($beffectsample);
			
			# calculate hp
			my ($amajor, $aminor, $bmajor, $bminor) = (0) x 4;
			if($aref >= $amut)
			{
				$amajor = $aref * 2 + $ahet;
				$aminor = $amut * 2 + $ahet;
			}else{
				$amajor = $amut * 2 + $ahet;
				$aminor = $aref * 2 + $ahet;
			}
			if($bref >= $bmut)
			{
				$bmajor = $bref * 2 + $bhet;
				$bminor = $bmut * 2 + $bhet;
			}else{
				$bmajor = $bmut * 2 + $bhet;
				$bminor = $bref * 2 + $bhet;
			}
			push @ahp, 2 * $amajor * $aminor / (($amajor + $aminor) ** 2);
			push @bhp, 2 * $bmajor * $bminor / (($bmajor + $bminor) ** 2);
		}
		my $final_fst = &ave(@allpi) != 0 ? 1 - &ave(@avepi) / &ave(@allpi) : 0;
		if($final_fst >= 1)
		{
			$final_fst = "1.0000";
		}elsif($final_fst <= 0){
			$final_fst = "0.0000";
		}else{
			$final_fst = sprintf("%.4f", $final_fst);
		}
        my $piratio = (&ave(@api))==0 ? 0 : &ave(@bpi)/&ave(@api);
		my $o = join("\t", "$_\t$rawlen", &ave(@aomega), &ave(@bomega), &ave(@api), &ave(@bpi), $piratio, &ave(@allpi), $final_fst, &ave(@atajimad), &ave(@btajimad), &ave(@ahp), &ave(@bhp));
		print OO $o."\n";
	}
}

sub ave{
	my (@a) = @_;
	my ($sum) = (0) x 1;
	foreach my $i(@a)
	{
			$sum += $i;
	}	
	return sprintf("%.6f", $sum / $opts{w});
}

sub sdd{
	my ($n) = @_;
	my ($a1, $a2);
	for(my $i = 1; $i < $n; $i ++)
	{
		$a1 += 1 / $i;
		$a2 += 1 / ($i * $i);
	}
	my $b1 = ($n + 1) / (3 * ($n - 1));
	my $b2 = 2 * ($n * $n + $n + 3) / (9 * $n * ($n - 1));
	my $c1 = $b1 - 1 / $a1;
	my $c2 = $b2 - ($n + 2) / ($a1 * $n) + $a2 / ($a1 * $a1);
	my $e1 = $c1 / $a1;
	my $e2 = $c2 / ($a1 * $a1 + $a2);
	my $value = sqrt($e1 * $n + $e2 * $n * ($n - 1));
	return $value;
}

sub tt{
	my ($N) = @_;
	my $sum;
	for(my $i = $N; $i > 0; $i --)
	{
		$sum += 1 / $i;
	}
	return $sum;
}