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, 14:01, 17 October 2012
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| * 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 than 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. |
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| == Usage == | | == Usage == |