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SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. BAM format is the compressed binary version of SAM format. Further information about it these formats can be read found in the SAM format specifications document. BAM format is the compressed binary version of SAM format.

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The Flux Capacitor needs the SAM input file to be indexed. The index is needed to access every locus indipendently, without the need to sequentially read the whole file. For this reason only BAM files are supported.

The BAM file must be sorted by the reference ID and then the leftmost coordinate before indexing (see SAM format specification above). The index file has to be placed in the same folder as the BAM file.

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