SAMTOOLS

Record added by Jurg Ott (the original Rockefeller list)

Full Name

Sequence Alignment/Map TOOLS

Description

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. The parts that relevant to genetic analysis include SNP and indel callings.

Author

  • Heng Li (Broad Institute)

  • Richard Durbin (Wellcome Trust Sanger Institute) et al.

    URL

    http://samtools.sourceforge.net/

    Language

    C, C++, Java, Perl, Python, Ruby, Common LISP, Haskell

    Reference

    Li, Handsaker, Wysoker, Fennell, Ruan, Homer, Marth, Abecasis, Durbin, and 1000 Genome Project Data Processing Subgroup (2009), “The sequence alignment/map (SAM) format and SAMtools”, Bioinformatics, 25:2078-2079.