VarScan statistics

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Citations per year

Citations chart

Popular tool citations

chevron_left SNP detection Low-frequency SNV detection De novo mutation detection SNV detection Somatic CNA detection SNP detection Indel detection CNV detection Indel detection chevron_right
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Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases


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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



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Publications for VarScan

VarScan in pipelines

PMCID: 5829066
PMID: 29527200
DOI: 10.3389/fmicb.2018.00322

[…] pmk-1 (nz_cp008929) using bwa-sw (version 0.7.13-r1126, default parameters) (li and durbin, ). the reference genome was selected using refrank (version 1.0.0; see below). snps were called using varscan v2.3 (koboldt et al., ) and variant positions were filtered using snpfilter (version 2.2.0; see below). based on the aligned variant positions maximum-likelihood trees were calculated using […]

PMCID: 5891033
PMID: 29590105
DOI: 10.1371/journal.pbio.2004444

[…] “bowtie2” [] with the parameter set “very fast” (section a in ). overall mean coverage was 886x and varied across samples from 202x to 1,497x (section a in ). variant calling was carried out using varscan version 2.3.9 []. more details can be found in section a of ., we thank s. allesina, j. bergelson, m. kreitman, v. morley, and c. pfister for comments on earlier versions of the text. […]

PMCID: 5923232
PMID: 29703930
DOI: 10.1038/s41598-018-24967-y

[…] for all the samples using fastqc with raw reads checked for quality, gc bias, k-mer quality, duplication levels. calling and filtering of variants and indels was done by a wide number of tools, viz. varscan, annovar and vt which compares known sites in variant databases with parameters set (fig. ) to establish sensitivity and specificity of variants calling. mutations were counted […]

PMCID: 5923232
PMID: 29703930
DOI: 10.1038/s41598-018-24967-y

[…] a number of exome sites, low-coverage sites and large deletions could not be validated (supplementary table ). the initial indel call yielded average depth coverage of 33.9264 and 40.9896 for vt and varscan respectively. we observed 63484 heterozygous variants which confirm that the variant calls with above thresholds were filtered across all samples. in addition, the low-coverage snps and indel […]

PMCID: 5928087
PMID: 29713003
DOI: 10.1038/s41467-018-04129-4

[…] 186 smc matched tumor/normal samples using varscan2 v2.4.1 in the paired mutation calling mode. parameters were selected based on the dream-3 setting of the false positive filter as recommended by varscan2. all germline and somatic mutations were annotated using the ensembl variant effect predictor. significantly mutated gene analysis was performed using mutsigcv v1.2 from the online […]

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VarScan in publications

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 […]

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 […]

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, […]

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 […]

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 […]

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VarScan institution(s)
Genome Institute at Washington University

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