Difference between revisions of "SNVMix"
m (Text replace - "MIT License" to "MIT") |
m (Text replace - "SNP discovery" to "SNP detection") |
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=Detects single nucleotide variants from next generation sequencing data. | |sw summary=Detects single nucleotide variants from next generation sequencing data. | ||
| − | |bio domain=SNP | + | |bio domain=SNP detection, |
|input format=Pileup | |input format=Pileup | ||
|language=C | |language=C | ||
Latest revision as of 15:43, 19 December 2015
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Application data |
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| Biological application domain(s) | SNP detection |
|---|---|
| Maintained? | Maybe |
| Input format(s) | Pileup |
| Programming language(s) | C |
| Licence | MIT |
Summary: Detects single nucleotide variants from next generation sequencing data.
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SNVMix is designed to detect single nucleotide variants from next generation sequencing data. SNVMix is a post-alignment tool. Given a pileup file (either Maq or Samtools format) as input and model parameters, SNVMix will output the probability that each position is one of three genotypes: aa (homozygous for the reference allele, where the reference is the genome the reads were aligned to), ab (heterozygous) and bb (homozygous for a non-reference allele). A tool for fitting the model using expectation maximization is also supplied (use -T option).
Links
References
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