|Biological application domain(s)||SNP discovery|
|Input format(s)||SAM, BAM|
|Software features||SNP calling|
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.
- Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L.. 2009. Bioinformatics
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