while(<INPUT>) {
  $linecount++ ; 
  next if $linecount <= $numHeaders;
  # ...
}
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Why not, but if the file is very large you're doing a $linecount incrementation and a test for every line in the file.

<INPUT> for 1..$numHeaders;
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is just reading the first $numHeaders lines of the file and throws them away, and you don't add any overhead for the rest of your file. And, BTW, the $. special variable contains the line count of the last read file handle, so that you don't need the $linecount incrementation.