sorry for bothering you all, i made a silly mistake and i rectified it :) thanks for all your suggestions. now that there are other methods also for me to look at from all your suggestions :)

the corrections i did was:
if(defined($variant)){ 
    foreach my $lis(@snplist){
        if($queryinfo[2] eq $lis){$flag_left=1;}
        elsif($queryinfo[3] eq $lis){$flag_right=1;}
    }

        if(($flag_left == 1) && ($flag_right == 1)){
        print OUT "$_\t$rs\n";
        $c++;
        $flag_left=0;$flag_right=0;
        }
          else{
            print OUT "$_\t-\n";
         }


  }

  else{
    print OUT "$_\t-\n";
  }
[download]

i should just add an else statement under if.. thats all :)