You also need to skip the comparison for the first line of data. 
#!/usr/bin/perl
use warnings;
use strict;
my $prev_l;
my $prev_p;
my $count = 0; ### add
while(<>){
  my $hitlength;
  my $prevalence;
 
  my $line = $_;  
  chomp $line;
  if ($line =~ /^[\d]/){
    my @hitline = split(/,/ , $line);
    $hitlength  = $hitline[4];
    $prevalence = $hitline[65];
    if( ($count++) and
        ($hitlength  == $prev_l) and
        ($prevalence == $prev_p) ){
        next;
    } else {
      print "$line\n";    
    }
    $prev_l = $hitlength;
    $prev_p = $prevalence;
  } 
}

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poj

In reply to Re: How to Save a variable outside of a loop by poj
in thread How to Save a variable outside of a loop by Calebros

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