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== 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 from 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 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.
* For ''de novo'' mutations, it is usually helpful to explore various mutation rate in addition to the default one (1.5x10-8). For depth lower than 30X for example, the support of ''de novo'' mutation will be weak given the low mutation rate of the default value. Trying higher values of mutation rates may be able to pick up these sites with low depth.
* For ''de novo'' mutations, it is usually helpful to explore various mutation rate in addition to the default one (1.5x10-8). For depth lower than 30X for example, the support of ''de novo'' mutation will be weak given the low mutation rate of the default value. Trying higher values of mutation rates may be able to pick up these sites with low depth.
== Usage ==
== Usage ==
