The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
VarScan: variant detection in massively parallel sequencing of individual and pooled samples
Open accessAbstract
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.
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Cites
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
The complete genome of an individual by massively parallel DNA sequencing
Wheeler, D. A., Srinivasan, M., Egholm, M., Shen, Y., Chen, L., McGuire, A., He, W., Chen, Y.-J., Makhijani, V., Roth, G. T., et al. (2008) · Nature · doi:10.1038/nature06884 · Cited by 1,838
Self-citationThe diploid genome sequence of an Asian individual
Wang, J., Wang, W., Li, R., Li, Y., Tian, G., Goodman, L., Fan, W., Zhang, J., Li, J., Zhang, J., et al. (2008) · Nature · doi:10.1038/nature07484 · Cited by 924 · cited 1×
“The genomes of a Nobel laureate (Wheeler et al., 2008), anonymous African and Asian individuals (Bentley et al., 2008; Wang et al., 2008), and both tumor and normal cells of a cancer patient (Ley et al., 2008) have been fully sequenced; ambitious efforts like the 1,000 Genomes Project aim to extend…”
Background
Cited by
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing
Ding, L., Ley, T. J., Larson, D. E., Miller, C. A., Koboldt, D. C., Welch, J. S., Ritchey, J. K., Young, M. A., Lamprecht, T., McLellan, M. D., et al. (2012) · Nature · doi:10.1038/nature10738 · Cited by 1,993
Repetitive DNA and next-generation sequencing: computational challenges and solutions
Treangen, T. J., & Salzberg, S. L. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3117 · Cited by 1,597
The origin and evolution of mutations in acute myeloid leukemia
Welch, J. S., Ley, T. J., Link, D. C., Miller, C. A., Larson, D. E., Koboldt, D. C., Wartman, L. D., Lamprecht, T. L., Liu, F., Xia, J., et al. (2012) · Cell · doi:10.1016/j.cell.2012.06.023 · Cited by 1,575
Self-citationHuman primary liver cancer–derived organoid cultures for disease modeling and drug screening
Broutier, L., Mastrogiovanni, G., Verstegen, M. M., Francies, H. E., Gavarró, L. M., Bradshaw, C. R., Allen, G. E., Arnes-Benito, R., Sidorova, O., Gaspersz, M. P., et al. (2017) · Nature Medicine · doi:10.1038/nm.4438 · Cited by 1,471
Metadata
- Authors
- Koboldt, D. C., Chen, K., Wylie, T., Larson, D. E., McLellan, M. D., Mardis, E. R., Weinstock, G. M., Wilson, R. K., & Ding, L.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-06-19
- Volume
- 25
- Issue
- 17
- Pages
- 2283-2285
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2161815151
- Cited by
- 1,348
- References
- 4
- FWCI
- 17.16
- Type
- journal article
- Language
- en
- Open access
- green
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- Koboldt, D. C., Chen, K., Wylie, T., Larson, D. E., McLellan, M. D., Mardis, E. R., Weinstock, G. M., Wilson, R. K., & Ding, L. (2009). VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. https://doi.org/10.1093/bioinformatics/btp373
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