SAM
From Just Solve the File Format Problem
Revision as of 03:51, 4 August 2020 by Dan Tobias (Talk | contribs)
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 @HD VN:1.6 SO:coordinate, 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.
