Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; [1] it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files. [2] [3]
BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments. [4] The goal of indexing is to retrieve alignments that overlap a specific location quickly without having to go through all of them. Before indexing, BAM must be sorted by reference ID and then leftmost coordinate. [5] BAM is in compressed BGZF format.
The structure of BAM files include a header section and an alignment section: [6]
Bam format uses 0-based coordinate system, where as SAM uses 1-based coordinate system. BAM can represent values in the range [−2^31 , 2^32). [5]
To view a list of sequencing and analysis tools that work with SAM/BAM click here.