You need to populate the hash inside the loop somehow. Here is one way: 
use warnings;
use strict;

my $counter = 0;
my %hash;
while (<DATA>) {
    my @splits = split;
    my $snp = $splits[0];
    $counter++ if not exists $hash{$snp};
    print "$counter $snp\n";
    $hash{$snp}++;
}

__DATA__
foo    abc
foo    cde
bar    xyz

[download]

Prints: 

1 foo
1 foo
2 bar

[download]

In reply to Re: only increment counter if the ID has not been seen before by toolic
in thread only increment counter if the ID has not been seen before by Anonymous Monk

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