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VarScan specifications


Unique identifier OMICS_00094
Name VarScan
Alternative name VarScan2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format Pileup
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, Perl, R
Computer skills Advanced
Version 2.3.7
Stability Stable
Maintained Yes


  • copynumber
  • mpileup2cns
  • somatic




No version available

Publications for VarScan

VarScan citations


Comparative Genomics Reveals the Core Gene Toolbox for the Fungus Insect Symbiosis

PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] comparative pipeline. The individual allele frequency was calculated using the read counts of the binary alignment map (BAM) files against the single-copy orthologs with the “pileup2snp” function of VarScan v2.3.9 () (default parameters were determined using a –min-coverage value of 10 and a P value of 0.05). The allele frequency value was then rounded to an integer value before being plotted wit […]


Comparative whole genome re sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions

PMCID: 5953909
PMID: 29766351
DOI: 10.1186/s12284-018-0224-3

[…] oincidence within genotype was no less than 80% for homozygous polymorphism mining. SNPs and MNPs were called using an in-house Perl script ‘SNiPer2’. Short Indel sites were called using the software VarScan2 version 2.3.9 with the command of somatic and the options of ‘--min-base-qual 0′. […]


Muver, a computational framework for accurately calling accumulated mutations

BMC Genomics
PMCID: 5944071
PMID: 29743009
DOI: 10.1186/s12864-018-4753-3

[…] 26× and 108× coverage, reducing the depth to a level more readily achieved in experiments likely to be analyzed using muver. To provide context for these values, we identified clonal differences with VarScan version 2.4.3 [] using the Somatic Mutation Calling workflow and VarDict version 1.5.1 []. Additionally, we called variants with HaplotypeCaller for the father and son individually, and combin […]


VAReporter: variant reporter for cancer research of massive parallel sequencing

BMC Genomics
PMCID: 5954270
PMID: 29764369
DOI: 10.1186/s12864-018-4468-5

[…] mparison, and visual interpretation of the genetic variants. VAReporter has the ability to accept heterogeneous variant call file (VCF) formats from state-of-the-art variant callers, such as GATK [], VarScan [], MuTect [] and VarDict [], and provides the most comprehensive list of support formats with respect to single and paired samples. A wide variety of biomedical databases, including dbSNP [], […]


Recurrent hotspot mutations in HRAS Q61 and PI3K AKT pathway genes as drivers of breast adenomyoepitheliomas

Nat Commun
PMCID: 5940840
PMID: 29739933
DOI: 10.1038/s41467-018-04128-5
call_split See protocol

[…] e performed using the Genome Analysis Toolkit (GATK). Somatic single nucleotide variants (SNVs) were identified using MuTect; small insertions and deletions (indels) were identified using Strelka and VarScan 2,, and further curated by manual inspection. Variants found with >5% global minor allele frequency in dbSNP (Build 137) or that were covered by <10 reads in the tumor or <5 reads in the germl […]


De novo activating mutations drive clonal evolution and enhance clonal fitness in KMT2A rearranged leukemia

Nat Commun
PMCID: 5932012
PMID: 29720585
DOI: 10.1038/s41467-018-04180-1

[…] on BaseSpace (Illumina) using a banded Smith–Waterman algorithm and Bedtools was used to calculate coverage. Mpileup files were created using SAMtools (1.3.1) and variant calling was performed using VarScan (2.4.1). Putative mutations were filtered based on quality and resultant variants were manually reviewed using Bambino. For calculations of mutant allele frequencies, the number of reads requi […]


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VarScan institution(s)
Genome Institute at Washington University

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