BAM Files

The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mb) produced by different sequencing platforms. SAM is a text format file that is human-readable. The Binary Alignment/Map (BAM) keeps the same information as SAM, but in a compressed, binary format that is only machine readable.

Detailed Description

The file naming convention for aligned reads in BAM format is as follows: SampleName_S#.bam (where # is the sample number determined by ordering in the sample sheet).

Go to samtools.sourceforge.net/SAM1.pdf to see the exact SAM specification.

BWA adds some custom fields to the BAM output. See bio-bwa.sourceforge.net/bwa.shtml#4 for a description.