SAM Tools A flexible generic format for storing nucleotide sequence alignment
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store manipulate store nucleotide alignment manipulate alignment alignment manipulator alignment

SAM Tools Description

A flexible generic format for storing nucleotide sequence alignment 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: · SAMtools is more consistent with the specification: a) '*' in the · QUAL field is allowed; b) the field separator is TAB only and SPACE · is treated as a character in a field; c) empty header is allowed. · Implemented GLFv3 support in pileup. · Fixed a severe bug in fixmate: strand information is wrongly · overwritten. · Fixed a bug in alignment retrieval: alignments bridging n*16384bp are · not correctly retrieved sometimes. · Fixed a bug in rmdup: segfault if unmapped reads are present. · Move indel_filter.pl to samtools.pl and improved the filtering by · checking the actual number of alignments containing indels. The indel · pileup line is also changed a little to make this filtration easier. · Fixed a minor bug in indexing: the bin number of an unmapped read is · wrongly calculated. · Added `flagstat' command to show statistics on the FLAG field. · Improved indel caller by setting the maximum window size in local · realignment. Changes in other utilities: · Fixed a bug in maq2sam: a tag name is obsolete. · Improvement to wgsim: a) added support for SOLiD read simulation; · b)show the number of substitutions/indels/errors in read name; · c)considerable code clean up. · Various converters: improved functionality in general. · Updated the example SAM due to the previous bug in fixmate.

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