SAM

SAM (Sequence Alignment/Map) is a data format used for mapping sequences of DNA. It is in text (tab-separated) form, while A companion format BAM is binary. It is classified as an alignment format, as is CRAM. This is as opposed to sequence-only, unaligned, formats such as FASTA and FASTQ.

Indexes associated with a SAM file are called SAI.

Identification
Files will often start with a header line (though this is technically optional), such as, where the VN parameter gives the version number of the format and this may be followed with a SO or G0 parameter giving sorting order or grouping of alignments.

Specifications

 * SAM/BAM specification
 * Optional fields (tags) specification

Links

 * Wikipedia article
 * HTS-Specs Github
 * samtools-devel mailing list