VarScan: variant detection in massively parallel sequencing of individual and pooled samples
By Daniel C. Koboldt, Ken Chen, T. Wylie, David E. Larson, M. McLellan, Elaine R. Mardis, George M. Weinstock, Richard K. Wilson, Li Ding. Bioinform., 2009
1,343 citations recorded by the source corpus.
Subfields: Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/9b37f308fc68930fa642b48b8ae95e6068d9c3a2
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Steven L. Salzberg
- Todd J. Treangen
- Daniel C. Koboldt
- Elaine R. Mardis
- Heng Li
- Richard Durbin
- Niranjan Nagarajan
- Mark A. DePristo
In Plant Science
- Niranjan Nagarajan
- Todd J. Treangen
- Steven L. Salzberg
- Richard Durbin
- Mark J. Daly
- G. McVean
- David Haussler
- Gerton A. Lunter
Citations in the corpus
- LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets (2012, background): “While approaches to correct for these have been studied, the majority of variant-calling methods have focused on low-coverage human re-sequencing data and diploid calls (14) (15) (16) with discrete frequencies of interest (i.e. 0, 0.5 and 1; a related set of methods are those tailored for calling di”
- Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study (2011, neutral): “php/MuTect), VarScan(29) (http://varscan.”
- Applications of next generation sequencing in molecular ecology of non-model organisms (2011, methodology): “GigaBayes (Hillier et al., 2008) and VarScan (Koboldt et al., 2009) represent examples of programs for SNP detection.”
- pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens (2016, methodology): “(2) VarScan Somatic version 2.2.6 [33, 34] was run with default parameters and the variant calls were filtered by GMS filter ‘ varscan-high-confidence filter version v1 ’ .”
- lobSTR: A short tandem repeat profiler for personal genomes (2012, background): “As of today, sequence analysis algorithms can detect almost any type of genetic variations, from SNPs (Goya et al. 2010) and indels (Koboldt et al. 2009; Goya et al. 2010) to CNVs and chromosomal translocations (Chen et al. 2009). lobSTR adds a new layerofinformationwithtens ofthousandsof…”
- Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection (2015, background): “We will keep leaderboards open indefinitely to allow rapid comparison of methods, and we hope journals will expect benchmarking on these data sets in reports of new somatic SNV detection algorithms.”
- VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. (2012, methodology): “Previously, we published VarScan (Koboldt et al. 2009), an algorithm for variant detection in next-generation sequencing”