Difference between revisions of "VarScan"
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|bio domain=SNP discovery, | |bio domain=SNP discovery, | ||
|maintained=Yes | |maintained=Yes | ||
| − | |input format=SAM, BAM, | + | |email address=dkoboldt@genome.wustl.edu |
| − | |output format=TXT, | + | |input format=SAM, BAM, |
| + | |output format=TXT, | ||
|sw feature=SNP calling | |sw feature=SNP calling | ||
| − | |language=Java, | + | |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. | 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. | ||
Revision as of 19:33, 3 December 2015
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Application data |
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| Biological application domain(s) | SNP discovery |
|---|---|
| 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.
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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.
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