note Riales <p>Nothing jumps out at me, but I am inclined to agree with your guess about the problem being in the last part of the code. Have you tried adding print statements before the chomp, before the substitution, and after the substitution?</p> <code> while (<$new_in_file>) { print "BEFORE CHOMP: $_\n"; chomp; next if $. == 1; # remove header line s/POS/SAMPLE/ if $. == 2; s/\s+/,/g if $. == 2; # replace whitespace with a comma on ID row next if $. >= 3 and $. <= 9; # remove unwanted lines print "BEFORE SUBSTITUTION: $_\n"; s/\s+(\d)\|(\d)\S+/,$1 $2/g; # clean up the SNPs & put into CSV format print "AFTER SUBSTITUTION: $_\n"; print $new_out_file "$_\n"; } </code> 964788 964788