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== What is SAM ==

== What is SAM ==

The '''SAM Format''' is a text format for storing aligned reads in a series of tab delimited ASCII columns.  

The '''SAM Format''' is a text format for storing sequence data in a series of tab delimited ASCII columns.  

Most often it is generated as a human readable projection of its sister [[BAM]] format, which can store data in a compact, indexed, binary representation.  

Most often it is generated as a human readable version of its sister [[BAM]] format, which stores the same data in a compressed, indexed, binary form.

 

Currently, most SAM format data is output from aligners that read FASTQ files and assign the sequences to a position with respect to a genome.  In the future, SAM will also be used to archive unaligned sequence data generated directly from sequencing machines.

The current definition of the format is at [[http://samtools.sourceforge.net/SAM1.pdf BAM/SAM Specification]].

The current definition of the format is at [[http://samtools.sourceforge.net/SAM1.pdf BAM/SAM Specification]].

== What Information is in SAM & BAM ==

== What Information is in SAM & BAM ==