The code -- revised version by GrandFather. 

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my $data = '/DATA/alignment.fas';
open my $inFile, '<', $data or die "Failed at opening $data: $!\n";

# Populate the info hash with GIs as keys and sequences as values
my $humanGi;
my $accession;
my $gi;    # Current gi while reading sequences
my %info;

while (<$inFile>) {
    my $line = $_;
    chomp $line;
    last if m!END!;

    if ($line =~ m/(HUMAN|Homo)/) {
        ($humanGi, $accession) = $line =~ m/^\S+\|(\d+)\|\w+\|(\S{6}?)/;
    }

    if ($line =~ m/^\S+\|(\d+)/) {
        $gi = $1 if defined $1;
    } else {
        $info{$gi} = $line;
    }
}
print Dumper (\%info);
close $inFile;

my $data2 = '/DATA/variantList.txt';
open $inFile, '<', $data2 or die "Failed at opening $data2: $!\n";

my $data3 = '/DATA/pathogenList.txt';
open my $outFile, '>', $data3 or die "Failed at opening $data3: $!\n";

print $outFile
    "This is [GI: $humanGi] and [Accession: $accession]\nVARIANT\t\tPOTENTIAL\t\tPD\n";

while (defined (my $Variant = <$inFile>)) {
    # Grab a variant from the file (in this example: P82L)
    chomp $Variant;

    my ($source, $position, $sink) = split /(\d+)(\w)/, $Variant;

    # Check whether HS has the source (i.e., P) at the given position (i.e., 82)
    #my @char = split //, $info{$humanGi};
    #my $target = $char[$position - 1];
    my @VariantList;
    my @PDList;

    # Scan the rest of the sequences to check what amino acid they have at
    # the given position
    foreach my $gi (keys %info) {
        my @char2 = split //, $info{$gi};
        my $potential = $char2[$position - 1];

        push @VariantList, "${potential}{$gi}";

        if ($potential eq $sink) {
            # Note the cases where we observe the sink (i.e., L) at this position

            push @PDList, "${potential}{$gi}";
        }
    }

    print $outFile "$Variant\t@VariantList\t@PDList\n";
}
close $inFile;
close $outFile;