title: VarScan: variant detection in massively parallel sequencing of individual and pooled samples.
abstract: Massively parallel sequencing technologies hold incredible promise for the study of DNA sequence variation, particularly the identification of variants affecting human disease. The unprecedented throughput and relatively short read lengths of Roche/454, Illumina/Solexa, and other platforms have spurred development of a new generation of sequence alignment algorithms. Yet detection of sequence variants based on short read alignments remains challenging, and most currently available tools are limited to a single platform or aligner type. We present VarScan, an open source tool for variant detection that is compatible with several short read aligners. We demonstrate VarScan's ability to detect SNPs and indels with high sensitivity and specificity, in both Roche/454 sequencing of individuals and deep Illumina/Solexa sequencing of pooled samples.
authors: The Genome Center at Washington University School of Medicine, St Louis, MO 63108, USA. dkoboldt@genome.wustl.edu
authors: Daniel C
authors: DC
authors: Koboldt
authors: Ken
authors: K
authors: Chen
authors: Todd
authors: T
authors: Wylie
authors: David E
authors: DE
authors: Larson
authors: Michael D
authors: MD
authors: McLellan
authors: Elaine R
authors: ER
authors: Mardis
authors: George M
authors: GM
authors: Weinstock
authors: Richard K
authors: RK
authors: Wilson
authors: Li
authors: L
authors: Ding
mesh_terms: D019295:Computational Biology / Q000379:methods*; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software