Difference between revisions of "SAMtools"
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=Various utilities for processing alignments in the SAM format, including variant calling and alignment viewing. | |sw summary=Various utilities for processing alignments in the SAM format, including variant calling and alignment viewing. | ||
− | |bio domain=SNP | + | |bio domain=SNP detection, |
− | |bio method= | + | |bio method=Modelling and simulation, , Sequence assembly visualisation |
|maintained=Yes | |maintained=Yes | ||
|input format=SAM, BAM | |input format=SAM, BAM | ||
− | |output format=SAM, BAM, VCF | + | |output format=SAM, BAM, VCF, Pileup |
|sw feature=Integrated solution, API | |sw feature=Integrated solution, API | ||
|language=C | |language=C | ||
− | |licence=MIT | + | |licence=MIT |
}} | }} | ||
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/ | 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/ | ||
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== Manual == | == Manual == | ||
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{{Links}} | {{Links}} | ||
{{References}} | {{References}} | ||
{{Link box}} | {{Link box}} |
Latest revision as of 00:20, 20 December 2015
Application data |
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Biological application domain(s) | SNP detection |
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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.
"Error: no local variable "counter" was set." is not a number.
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
To add a reference for SAMtools, enter the PubMed ID in the field below and click 'Add'.
[ edit box ]
Search for "SAMtools" in the SEQanswers forum / BioStar or:
Web Search | Wiki Sites | Scientific |
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