SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment.
SAM tools provide efficient utilities on manipulating alignments in SAM format.
Here are some key features of "SAM Tools":
· Is flexible enough to store all the alignment information generated by various alignment programs;
· Is simple enough to be easily generated by alignment programs or converted from existing alignment formats;
· Is compact in file size;
· Allows most of operations on the alignment to work on a stream without loading the whole alignment into memory;
· Allows the file to be indexed by genomic position to efficiently retrieve all reads aligning to a locus.
What's New in This Release: [ read full changelog ]
· Many important bugfixes and contributions by many people. Thanks to all!
· Performance improvements (multi-threading)
· Important changes in calling
· New annotations useful for filtering (RPB, HWE, QBD, MDV)
· New tools, bamcheck and plot-bamcheck
· New features in samtools tview