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22 lines
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22 lines
1 KiB
Text
SAM (Sequence Alignment/Map) format is a generic format for storing
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large nucleotide sequence alignments. SAM aims to be a format that:
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- Is flexible enough to store all the alignment information generated
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by various alignment programs
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- Is simple enough to be easily generated by alignment programs or
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converted from existing alignment formats
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- Is compact in file size
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- Allows most of operations on the alignment to work on a stream
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without loading the whole alignment into memory
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- Allows the file to be indexed by genomic position to efficiently
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retrieve all reads aligning to a locus.
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SAM Tools provide various utilities for manipulating alignments in the
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SAM format, including sorting, merging, indexing and generating
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alignments in a per-position format.
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Publication:
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Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N.,
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Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data
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Processing Subgroup (2009) The Sequence alignment/map (SAM) format and
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SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]
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