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

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.

SUBMITTER: Koboldt DC

PROVIDER: S-EPMC2734323 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature

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

Koboldt Daniel C DC Chen Ken K Wylie Todd T Larson David E DE McLellan Michael D MD Mardis Elaine R ER Weinstock George M GM Wilson Richard K RK Ding Li L

Bioinformatics (Oxford, England) 20090619 17

<h4>Summary</h4>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 availabl ...[more]

PMID: 19542151

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