VarScan statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool VarScan
info

Tool usage distribution map

This map represents all the scientific publications referring to VarScan per scientific context
info info

Associated diseases

This word cloud represents VarScan usage per disease context
info

Popular tool citations

chevron_left SNP detection Somatic CNA detection De novo mutation detection SNP detection SNV detection Low-frequency SNV detection Indel detection CNV detection Indel detection chevron_right
Want to access the full stats & trends on this tool?

Protocols

VarScan specifications

Information


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

Subtools


  • copynumber
  • mpileup2cns
  • somatic

Download


galaxy.png
debian.png
conda.png

Versioning


No version available

Publications for VarScan

VarScan citations

 (608)
library_books

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

2018
MBio
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 […]

library_books

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

2018
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′. […]

library_books

Muver, a computational framework for accurately calling accumulated mutations

2018
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 […]

library_books

VAReporter: variant reporter for cancer research of massive parallel sequencing

2018
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 [], […]

call_split

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

2018
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 […]

library_books

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

2018
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 […]


Want to access the full list of citations?
VarScan institution(s)
Genome Institute at Washington University

VarScan reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review VarScan