VarSim specifications

Information


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

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Publication for VarSim

VarSim in publications

 (6)
PMCID: 5591230
PMID: 28887485
DOI: 10.1038/s41598-017-10826-9

[…] that might be missed by the alignment-based approach. the low recovery rate of snvs by the assembly-based approach was due to inability of haplotype-resolved assembled contigs by soapdeno2., 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 […]

PMCID: 5537105
PMID: 28794828
DOI: 10.1016/j.csbj.2017.07.002

[…] 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 […]

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

[…] 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., as previously mentioned, nist genomic variants were used in the genome-aware approach. the publicly available snps […]

PMCID: 5192301
PMID: 28070503
DOI: 10.1155/2016/7983236

[…] important to identify significant somatic mutations from these variants. several tools have been developed to do this task for the analysis of cancer wes data, including somaticsniper [], mutect [], varsim [], and somvarius []., somaticsniper is a computational program that compares the normal and tumor samples to find out which mutations are unique to the tumor sample, hence predicted […]

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

[…] are those most often used, according to number of paper citations: art, curesim, dwgsim [], gemsim (including the the targeted sequencing functionality of wessim []), mason [], pirs, and sinc []. varsim [] is not explicitly listed as it is a wrapper around dwgsim and art., comparison of the main features of several existing read simulator packages., ×: feature is present in the simulator., *: […]


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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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