Sequence Alignment/Map Format Specification

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Sequence Alignment/Map Format SpecificationThe SAM/BAM Format Specification Working Group22 May 2018The master version of this document can be found printing is version b1ae9f9 from that repository, last modified on the date shown The SAM Format SpecificationSAM stands for Sequence Alignment/Map Format . It is a TAB-delimited text Format consisting of a headersection, which is optional, and an alignment section. If present, the header must be prior to the lines start with @ , while alignment lines do not. Each alignment line has 11 mandatory fields foressential alignment information such as mapping position, and variable number of optional fields for flexibleor aligner specific Specification is for version of the SAM and BAM formats. Each SAM and BAM file mayoptionally specify the version being used via the@HD VNtag. For full version history see Appendix explicitly specified elsewhere, all fields are encoded using 7-bit US-ASCII1in using the POSIX /C locale.

sequencing data, reads are indexed by the order in which they are sequenced. Linear alignment An alignment of a read to a single reference sequence that may include insertions, deletions, skips and clipping, but may not include direction changes (i.e., one portion of the alignment ... AS Genome assembly identifier. 8 ...

  Specification, Sequencing, Genomes