The header, which begins with the symbol This contains a series of information such as generic information relating to the file and its version, those relating to the ordering of the file as well as those relating to the genome reference.File structure: SAM file consists of two main parts:.File type: Text file in which the alignment information is reported in ASCII characters.So to be as clear as possible I thought of presenting these two types of files schematically. The SAM file are the first products of the alignment process, while the BAM is derived, in fact this contain the same alignment information present inside a SAM file but simply in a compressed way it is more accessible to the programs used for the call of variants or for the simple graphical display of the mapping of the reads on the reference. In short, these file are essential to obtain the so-called "call" of the variants existing between the genomes being compared.īut let's go in order. In any case, the SAM and BAM file are equally useful for identifying the polymorphisms that exist between a sequenced and a reference genome as well as with a third genome also aligned on the same reference, or even a fourth, a fifth and so on. These are extremely useful file as they are produced by the process of aligning (or mapping) reads on a reference genome, this is also called re-sequencing, although in my opinion this term is a bit misleading. In fact, today we talk about SAM file, or Sequence Alignment Map file, and its cousin BAM file, Binary Alignment Map file. I have decided to delight you with a new article that will go straight into the column "Files in bioinformatics", in which I talk about the most common and important file types used by bioinformaticians.
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