SAMtools

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Application data

Biological application domain(s) SNP detection
Principal bioinformatics method(s) Modelling and simulation, Sequence assembly visualisation
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


To add a reference for SAMtools, enter the PubMed ID in the field below and click 'Add'.


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