Difference between revisions of "SAMtools"
(Brief description from the SAMtools webpage) |
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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 | ||
|input format=SAM, BAM | |input format=SAM, BAM | ||
| − | |output format=SAM, BAM, VCF | + | |output format=SAM, BAM, VCF, Pileup |
| − | |sw feature=Integrated solution, | + | |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/ | ||
| − | + | ||
| + | == Manual == | ||
| + | {{Links}} | ||
| + | {{References}} | ||
| + | {{Link box}} | ||
Latest revision as of 00:20, 20 December 2015
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Application data |
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| 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.
"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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