From Genome Analysis Wiki
Jump to navigationJump to search
No change in size
, 14:03, 17 October 2012
Line 20: |
Line 20: |
| | | |
| == 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. |