We found a match
Your institution may have access to this item. Find your institution then sign in to continue.
- Title
VarScan: variant detection in massively parallel sequencing of individual and pooled samples.
- Authors
Koboldt, Daniel C; Chen, Ken; Wylie, Todd; Larson, David E; McLellan, Michael D; Mardis, Elaine R; Weinstock, George M; Wilson, Richard K; Ding, Li
- 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.
- Publication
Bioinformatics (Oxford, England), 2009, Vol 25, Issue 17, p2283
- ISSN
1367-4811
- Publication type
Journal Article
- DOI
10.1093/bioinformatics/btp373