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VarSim specifications


Unique identifier OMICS_06837
Name VarSim
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, Python
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


Publication for VarSim

VarSim citations


FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods

Genome Biol
PMCID: 5859555
PMID: 29559002
DOI: 10.1186/s13059-018-1404-6

[…] taSV ensemble approach across all SV types.To obtain more data for the training phase of FusorSV, we generated 30 simulated human genomes at 50X coverage with simple and disjoint homozygous SVs using Varsim []; however, when we compared the simulation data to the real human data, we observed huge disparity in similarity values (Additional file : Figure S4A and B), suggesting that the current Varsi […]


Direct comparison of performance of single nucleotide variant calling in human genome with alignment based and assembly based approaches

Sci Rep
PMCID: 5591230
PMID: 28887485
DOI: 10.1038/s41598-017-10826-9

[…] We used VarSim and ART to simulate short reads with a fixed variant pool. The variants were obtained from the VarSim website as described in the quick start demo ( […]


Scalability and Validation of Big Data Bioinformatics Software

Comput Struct Biotechnol J
PMCID: 5537105
PMID: 28794828
DOI: 10.1016/j.csbj.2017.07.002

[…] fy a subset of the data.There are a number of simulation packages available that can simulate read data, and provide a ‘ground truth’ VCF file for the expected output. Two such programs are ART , and VarSim . Such programs allow for the generation of large amounts of data to be tested. While partially addressing the ‘gold-standard’ issue of lack of data, there are additional sources of uncertainty […]


Gaining comprehensive biological insight into the transcriptome by performing a broad spectrum RNA seq analysis

Nat Commun
PMCID: 5498581
PMID: 28680106
DOI: 10.1038/s41467-017-00050-4

[…] in Ensembl reference annotation, in the NIST HC regions that overlap (expressed) exons identified using Cufflinks and in the NIST HC regions that overlap (expressed) exons identified using StringTie. Varsim was used to compare the predicted and known variants in a given region. […]


A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data

Int J Genomics
PMCID: 5192301
PMID: 28070503
DOI: 10.1155/2016/7983236

[…] a more probable set of candidate genes. MuTect has been widely used in Broad Institute cancer genomics studies.While SomaticSniper and MuTect require data from both paired cancer and normal samples, VarSim [] and SomVarIUS [] do not require a normal sample to call somatic mutations. Unlike most programs of its kind, VarSim [] uses a two-step process utilizing both simulation and experimental data […]


Simulating Next Generation Sequencing Datasets from Empirical Mutation and Sequencing Models

PLoS One
PMCID: 5125660
PMID: 27893777
DOI: 10.1371/journal.pone.0167047

[…] t contains software for deriving mutation and sequencing models, simulating sequencing data, and evaluating alignment and variant calling algorithms. In this regard NEAT could be easily confused with VarSim [], itself a powerful computational framework with similar functions. However, VarSim is a wrapper around other simulators, and thus inherits all their features and limitations. Indeed, VarSim […]

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VarSim institution(s)
Department of Electrical Engineering, Stanford University, Stanford, CA, USA; Department of Bioinformatics, Bina Technologies, Redwood City, CA, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Mayo Clinics, Department of Health Sciences Research, Chinahester, MN, USA; Department of Statistics, Stanford University, Stanford, CA, USA; Department of Health Research and Policy, Stanford University, Stanford, CA, USA

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