Hi, could you please use <readmore> tags for code of this length. Also consider to use perltidy to format your code.

The previous poster already gave you a fix, so I just want to give you a little advice:
Your construct:

if ($current_line[0] eq $key) {
              if ($current_line[1] == $position1) {
                  if ($current_line[2] ==1) {
                      if ($current_line[3] >= 3) {

          print join ("\t", $current_line[0],$current_line[1],$current
+_line[2],$current_line[3], "***",$key, $position1), "\n";
                   }
                }
              }
           }
[download]

is much tidier written this way:

if (   $current_line[0] eq $key 
    && $current_line[1] == $position1
    && $current_line[2] == 1
    && $current_line[3] >= 3)
{
    print join ("\t", @current_line[0..3], "***", $key, $position1), "
+\n";
}
[download]