Changes

== Additional Notes ==

== Additional Notes ==

* All GLF files (and BAM files) in the input have to have IDENTICAL chromosome orders. Polymutt will go through the chromosomes in the order until when one GLF file has a different chromosome than others. All results prior to that problematic chromosome are valid though.

* All GLF files (and BAM files) in the input have to have IDENTICAL chromosome orders. Polymutt will go through the chromosomes in the order until when one GLF file has a different chromosome from others. All results prior to that problematic chromosome are valid though.

** If you do have different orders or even different number of chromosomes in the BAM files, you can create GLF files for individual chromosomes and run polymutt on matched chromosomes.

** If you do have different orders or even different number of chromosomes in the BAM files, you can create GLF files for individual chromosomes and run polymutt on matched chromosomes.

* For ''de novo'' mutations, the current version can only take GLF files and only detect single nucleotide mutations. It does not call ''de novo'' mutations on X, Y and MT chromosomes, and please ignore records in these non-autosomes. Indels are not handled either.

* For ''de novo'' mutations, the current version can only take GLF files and only detect single nucleotide mutations. It does not call ''de novo'' mutations on X, Y and MT chromosomes, and please ignore records in these non-autosomes. Indels are not handled either.