VarScan: variant detection in massively parallel sequencing of individual and pooled samples Export

@article{citeulike:4925254, abstract = {Summary: 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. Availability and Implementation: Source code and documentation freely available at http://genome.wustl.edu/tools/cancer-genomics implemented as a Perl package and supported on Linux/UNIX, MS Windows and Mac OSX. Contact: dkoboldt@genome.wustl.edu Supplementary information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btp373}, author = {Koboldt, Daniel C. and Chen, Ken and Wylie, Todd and Larson, David E. and McLellan, Michael D. and Mardis, Elaine R. and Weinstock, George M. and Wilson, Richard K. and Ding, Li}, citeulike-article-id = {4925254}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp373}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/25/17/2283.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/25/17/2283.full.pdf}, citeulike-linkout-3 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/17/2283}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19542151}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19542151}, day = {1}, doi = {10.1093/bioinformatics/btp373}, issn = {1460-2059}, journal = {Bioinformatics}, keywords = {bioinformatics, methods, nextgensequencing, resequencing, snp, solexa}, month = {September}, number = {17}, pages = {2283--2285}, posted-at = {2009-07-01 18:57:13}, priority = {2}, title = {VarScan: variant detection in massively parallel sequencing of individual and pooled samples}, url = {http://dx.doi.org/10.1093/bioinformatics/btp373}, volume = {25}, year = {2009} }

TY - JOUR ID - citeulike:4925254 L3 - citeulike-article-id:4925254 N2 - Summary: 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. Availability and Implementation: Source code and documentation freely available at http://genome.wustl.edu/tools/cancer-genomics implemented as a Perl package and supported on Linux/UNIX, MS Windows and Mac OSX. Contact: dkoboldt@genome.wustl.edu Supplementary information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btp373 IS - 17 JF - Bioinformatics SN - 1460-2059 EP - 2285 TI - VarScan: variant detection in massively parallel sequencing of individual and pooled samples VL - 25 SP - 2283 KW - bioinformatics KW - methods KW - nextgensequencing KW - resequencing KW - snp KW - solexa AU - Koboldt, Daniel AU - Chen, Ken AU - Wylie, Todd AU - Larson, David AU - McLellan, Michael AU - Mardis, Elaine AU - Weinstock, George AU - Wilson, Richard AU - Ding, Li PY - 2009/09/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btp373 ER -