Difference between revisions of "VarScan"
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=VarScan, an open source tool for variant detection that is compatible with several short read align-ers. | |sw summary=VarScan, an open source tool for variant detection that is compatible with several short read align-ers. | ||
| + | |bio domain=SNP detection, | ||
| + | |maintained=Yes | ||
| + | |email address=dkoboldt@genome.wustl.edu | ||
| + | |input format=SAM, BAM, | ||
| + | |output format=TXT, | ||
| + | |sw feature=SNP calling | ||
| + | |language=Java, | ||
}} | }} | ||
| − | + | VarScan is a platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency. | |
| + | {{Links}} | ||
| + | {{References}} | ||
| + | {{Link box}} | ||
Latest revision as of 15:48, 19 December 2015
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Application data |
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| Biological application domain(s) | SNP detection |
|---|---|
| Maintained? | Yes |
| Input format(s) | SAM, BAM |
| Output format(s) | TXT |
| Software features | SNP calling |
| Programming language(s) | Java |
| Contact: | dkoboldt@genome.wustl.edu |
Summary: VarScan, an open source tool for variant detection that is compatible with several short read align-ers.
"Error: no local variable "counter" was set." is not a number.
VarScan is a platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency.
Links
References
To add a reference for VarScan, enter the PubMed ID in the field below and click 'Add'.
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