Changes

** If you do have different orders or even different numbers 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 numbers 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.

* Some of the features will be implemented in future versions if needed.

* Some of the features will be implemented in future versions.

== Usage ==

== Usage ==