SAMtools

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Application data

Biological application domain(s) SNP discovery
Principal bioinformatics method(s) Simulation, Programming Library, Assembly visualization
Maintained? Yes
Input format(s) SAM, BAM
Output format(s) SAM, BAM, VCF, Pileup
Software features Integrated solution, API
Programming language(s) C
Licence MIT

Summary: Various utilities for processing alignments in the SAM format, including variant calling and alignment viewing.

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. See http://samtools.sourceforge.net/


Manual

Links


References

  1. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. Bioinformatics
  2. Li H. 2011. Bioinformatics


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