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Popular tool citations

chevron_left De novo mutation detection SNP detection SNV detection SNP detection Low-frequency SNV detection Somatic CNA detection Indel detection CNV detection Indel detection chevron_right

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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 […]


Programmable sequential mutagenesis by inducible Cpf1 crRNA array inversion

PMCID: 5954137
PMID: 29765043
DOI: 10.1038/s41467-018-04158-z

[…] following manufacturer protocols. reads were mapped to the mm10 or hg38 genome using bwa-mem, with settings -t 8 -w 200. after identification of indel variants using the pileup2indel function in varscan v2.3.9, a 1% variant frequency threshold was to identify high confidence variants for npf and dvf experiments. a less stringent 0.2% variant frequency threshold was used for the tsg-immune […]


Muver, a computational framework for accurately calling accumulated mutations

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

[…] 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, […]


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

PMCID: 5940840
PMID: 29739933
DOI: 10.1038/s41467-018-04128-5

[…] 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 […]


The utilization of next generation sequencing to detect somatic mutations and predict clinical prognosis of Chinese non small cell lung cancer patients

PMCID: 5951221
PMID: 29780256
DOI: 10.2147/OTT.S155995

[…] with the burrows-wheeler aligner., local alignment optimization, mark duplication, and variant calling were performed using genome analysis toolkit 3.2, picard (, and varscan. gene rearrangements were called with fusion and chromosomal translocation enumeration and recovery algorithm (factera), and copy number variation was analyzed with an in-house algorithm […]


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

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 […]

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VarScan institution(s)
Genome Institute at Washington University

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