Anonymous Monk,
This is how your code probably should be written based on what little I understand.

#!/usr/bin/perl
use strict;
use warnings;

my $in_file  = $ARGV[0] or die "Usage: <file1> <file2>";
my $in2_file = $ARGV[1] or die "Usage: <file2> <file2>";

open(my $fh, '<', $in_file) or die "Unable to open '$in_file' for read
+ing: $!";

my %bead;
while (<$in_file>) {
    chomp;
    my ($snp, $chr, $beadpoolid) = split /,/;
    $bead{$snp} = $beadpoolid;
}

open($fh, '<', $in2_file) or die "Unable to open '$in2_file' for readi
+ng: $!";
while (<$fh>) {
    next if ! /^SNP\s+Coor/;
    chomp; 
    my ($snp, $coor, $allele, @int) = split /\t/;
    next if ! $bead{$snp};
    print join("\t", $bead{$snp}, $snp, @int), "\n";
}
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