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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 ==
The alignment section contains the information for each sequence about where/how it aligns to the reference genome.
The alignment section contains the information for each sequence about where/how it aligns to the reference genome.
=== What Information Does SAM/BAM Have for an Alignment ===
=== What Information Does SAM/BAM Have for an Alignment ===
* the query quality for this alignment, [[SAM#What is QUAL?|QUAL]], one for each base in the query sequence.
* the query quality for this alignment, [[SAM#What is QUAL?|QUAL]], one for each base in the query sequence.
* Additional optional information is also contained within the alignment, [[SAM#What are TAGs?|TAGs]]. A bunch of different information can be stored here and they appear as key/value pairs. See the spec for a detailed list of commonly used tags and what they mean.
* Additional optional information is also contained within the alignment, [[SAM#What are TAGs?|TAGs]]. A bunch of different information can be stored here and they appear as key/value pairs. See the spec for a detailed list of commonly used tags and what they mean.
==== What is a CIGAR? ====
==== What is a CIGAR? ====
The POS indicates that the read aligns starting at position 5 on the reference.
The POS indicates that the read aligns starting at position 5 on the reference.
The CIGAR says that the first 3 bases in the read sequence align with the reference. The next base in the read does not exist in the reference. Then 3 bases align with the reference. The next reference base does not exist in the read sequence, then 5 more bases align with the reference. Note that at position 14, the base in the read is different than the reference, but it still counts as an M since it aligns to that position.
The CIGAR says that the first 3 bases in the read sequence align with the reference. The next base in the read does not exist in the reference. Then 3 bases align with the reference. The next reference base does not exist in the read sequence, then 5 more bases align with the reference. Note that at position 14, the base in the read is different than the reference, but it still counts as an M since it aligns to that position.
==== What is QUAL? ====
==== What is QUAL? ====
So, for SAM, the QUAL field is:
So, for SAM, the QUAL field is:
<math>QUAL = (-10 \log_{10}p) + 33</math>
<math>QUAL = (-10 \log_{10}p) + 33</math>
Phred Quality is also found in a FASTQ file, described here: http://en.wikipedia.org/wiki/FASTQ_format#Quality
==== What are TAGs? ====
==== What are TAGs? ====
== Example SAM ==
== Example SAM ==
