The Sequence Alignment/Map format and SAMtools

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  • Heng Li
    1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, 2Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA, 3Beijing Institute of Genomics, Chinese Academy of Science, Beijing 100029, China, 4Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, 5Department of Biology, Boston College, Chestnut Hill, MA 02467, 6Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA and 7http://1000genomes.org
  • Bob Handsaker
    1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, 2Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA, 3Beijing Institute of Genomics, Chinese Academy of Science, Beijing 100029, China, 4Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, 5Department of Biology, Boston College, Chestnut Hill, MA 02467, 6Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA and 7http://1000genomes.org
  • Alec Wysoker
    1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, 2Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA, 3Beijing Institute of Genomics, Chinese Academy of Science, Beijing 100029, China, 4Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, 5Department of Biology, Boston College, Chestnut Hill, MA 02467, 6Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA and 7http://1000genomes.org
  • Tim Fennell
    1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, 2Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA, 3Beijing Institute of Genomics, Chinese Academy of Science, Beijing 100029, China, 4Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, 5Department of Biology, Boston College, Chestnut Hill, MA 02467, 6Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA and 7http://1000genomes.org
  • Jue Ruan
    1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, 2Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA, 3Beijing Institute of Genomics, Chinese Academy of Science, Beijing 100029, China, 4Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, 5Department of Biology, Boston College, Chestnut Hill, MA 02467, 6Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA and 7http://1000genomes.org
  • Nils Homer
    1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, 2Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA, 3Beijing Institute of Genomics, Chinese Academy of Science, Beijing 100029, China, 4Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, 5Department of Biology, Boston College, Chestnut Hill, MA 02467, 6Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA and 7http://1000genomes.org
  • Gabor Marth
    1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, 2Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA, 3Beijing Institute of Genomics, Chinese Academy of Science, Beijing 100029, China, 4Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, 5Department of Biology, Boston College, Chestnut Hill, MA 02467, 6Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA and 7http://1000genomes.org
  • Goncalo Abecasis
    1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, 2Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA, 3Beijing Institute of Genomics, Chinese Academy of Science, Beijing 100029, China, 4Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, 5Department of Biology, Boston College, Chestnut Hill, MA 02467, 6Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA and 7http://1000genomes.org
  • Richard Durbin
    1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, 2Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA, 3Beijing Institute of Genomics, Chinese Academy of Science, Beijing 100029, China, 4Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, 5Department of Biology, Boston College, Chestnut Hill, MA 02467, 6Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA and 7http://1000genomes.org

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<jats:title>Abstract</jats:title> <jats:p>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.</jats:p> <jats:p>Availability:  http://samtools.sourceforge.net</jats:p> <jats:p>Contact:  rd@sanger.ac.uk</jats:p>

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  • Bioinformatics

    Bioinformatics 25 (16), 2078-2079, 2009-06-08

    Oxford University Press (OUP)

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