VarScan Tool name | VarScan |
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URL |
http://varscan.sourceforge.net/ |
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Important features | 1. VarScan is able to detect SNPs and indels from both Solexa and Roche platforms.
2. Unlike currently available variant detection tools, VarScan is compatible with several read aligners (BLAT, Newbler, cross_match, Bowtie and Novoalign) and calls variants in both individual and pooled samples.
3. As an input VarScan requires an alignment file. As an output, user gets reports of SNPs, insertions and deletions with their chromosomal coordinates, alleles, flanking sequence and read counts. |
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Citations | Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. VarScan: variant detection in massively parallel sequencing of individual and pooled samples.
Bioinformatics. 2009 Sep 1;25(17):2283-5. Epub 2009 Jun 19. PMID: 19542151 |
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Year of publication | 2009 |
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Rank by usage frequency | 100 |
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Comments | |
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Function | SNP discovery, Indel discovery |
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Category | Free, Downloadable |
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License | |
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Status | |
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Input file format | pileup file |
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Output file format | |
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Operating system | Windows 32/64bit
Linux/Unix 32/64bit
Mac OS X 32/64bit |
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Operating language | JAVA |
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Platform | Roche 454
Illumina/Solexa
ABI SOLiD |
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Maintained by | Washington University in St. Louis
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Downloadable file format | |
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Submission file format | |
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