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SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Further information about it can be read in the SAM format specifications document.

Info

For the SAM format, the 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 used as input for the Flux Capacitor should be sorted by genomic position and indexed. The index file has to be placed in the same folder as the BAM file.

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