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. 2009 Aug 15;25(16):2078-9.
doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8.

The Sequence Alignment/Map format and SAMtools

Heng Li1, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup
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Free PMC article

The Sequence Alignment/Map format and SAMtools

Heng Liet al. Bioinformatics. .
Free PMC article

Abstract

Summary:The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.

Availability:http://samtools.sourceforge.net.

Figures

Fig. 1.
Fig. 1.
Example of extended CIGAR and the pileup output. (a) Alignments of one pair of reads and three single-end reads. (b) The corresponding SAM file. The ‘ @SQ’ line in the header section gives the order of reference sequences. Notably, r001is the name of a read pair. According to FLAG163 (=1 + 2 + 32 + 128), the read mapped to position 7 is the second read in the pair (128) and regarded as properly paired (1 + 2); its mate is mapped to 37 on the reverse strand (32). Read r002has three soft-clipped (unaligned) bases. The coordinate shown in SAM is the position of the first aligned base. The CIGAR string for this alignment contains a P(padding) operation which correctly aligns the inserted sequences. Padding operations can be absent when an aligner does not support multiple sequence alignment. The last six bases of read r003map to position 9, and the first five to position 29 on the reverse strand. The hard clipping operation Hindicates that the clipped sequence is not present in the sequence field. The NMtag gives the number of mismatches. Read r004is aligned across an intron, indicated by the Noperation. (c) Simplified pileup output by SAMtools. Each line consists of reference name, sorted coordinate, reference base, the number of reads covering the position and read bases. In the fifth field, a dot or a comma denotes a base identical to the reference; a dot or a capital letter denotes a base from a read mapped on the forward strand, while a comma or a lowercase letter on the reverse strand.
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