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BAM File Format - Description


BAM is the compressed binary version of the Sequence Alignment/Map (SAM) format, a generic format for storing large nucleotide sequence alignments. A detailed description of the BAM/SAM format can be found on the SAM Tools web site: http://samtools.sourceforge.net.

Indexing

When uploading BAM files using the 'GMS' or 'GGA' options in the BAM file upload dialog they are required to be sorted by position and indexed. The BAM index file should be named by appending '.bai' to the BAM file name and it must reside in the same directory as the BAM file. When uploading BAM files using the 'local' option you don't have to provide the index file, it will be generated automatically.

Chromosome names

The chromosome names have to be in one of the following notations:

Note that Genomatix allows both 'M' and 'MT' as name for the mitochondrial chromsomes.

Invalid chromosomes

BAM files containing chromosomes named not compliant with the notations mentioned above can still be imported, but those chromosomes will be skipped for analyses conducted with such BAM files. The same goes for the length of a chromosome, if it differs from the length associated with the selected ElDorado version/genome build, then this chromosome will also be considdered as invalid and therefore won't be used for analyses.

On the special treatment of BAM files regarding the Project Management

BAM files can be very large! Therefore, when importing them via the 'GMS' or 'GGA' option of the BAM file upload dialog only meta information will be stored in the Project Management, e.g. the path to the original BAM file. Each GGA tool/program that accepts BAM files as input will try to fetch the actual BAM data directly from the original BAM file location. If you delete the original BAM file on the GMS or the GGA mounted device, then it will not be available for the GGA tools/programs anymore. On the other hand: the original BAM file won't be touched when you delete the corresponding BAM file entry in the Project Management.
The BAM file import via the 'local' option works just like the BED file import, i.e. the BAM file itself will be stored in the Project Management.