Record added by Jurg Ott (the original Rockefeller list)
Sequence Alignment/Map TOOLS
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.
Heng Li (Broad Institute)
Richard Durbin (Wellcome Trust Sanger Institute) et al.
C, C++, Java, Perl, Python, Ruby, Common LISP, Haskell
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.