VarScan

Application data
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

Summary: VarScan, an open source tool for variant detection that is compatible with several short read align-ers.

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

• VarScan Homepage [ edit link ]

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References

1. Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L.. 2009. Bioinformatics

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