VarScan 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

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Publications for VarScan

VarScan IN pipelines

 (30)
2018
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, 2009). the reference genome was selected using refrank (version 1.0.0; see below). snps were called using varscan v2.3 (koboldt et al., 2012) and variant positions were filtered using snpfilter (version 2.2.0; see below). based on the aligned variant positions maximum-likelihood trees were calculated […]

2018
PMCID: 5891033
PMID: 29590105
DOI: 10.1371/journal.pbio.2004444

[…] with the parameter set “very fast” (section a in s1 text). overall mean coverage was 886x and varied across samples from 202x to 1,497x (section a in s1 text). variant calling was carried out using varscan version 2.3.9 [63]. more details can be found in section a of s1 text., we thank s. allesina, j. bergelson, m. kreitman, v. morley, and c. pfister for comments on earlier versions […]

2018
PMCID: 5923232
PMID: 29703930
DOI: 10.1038/s41598-018-24967-y

[…] number of exome sites, low-coverage sites and large deletions could not be validated (supplementary table 1). 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 […]

2018
PMCID: 5930415
PMID: 29744043
DOI: 10.1186/s13756-018-0352-y

[…] from the mapping and tree calculation (see also results chapter). the reference genome was selected using refrank (version 1.0.0; see below). single nucleotide polymorphisms (snps) were called using varscan v2.3 [11] 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 raxml (version […]

2017
PMCID: 5298344
PMID: 28178345
DOI: 10.1371/journal.pone.0171221

[…] and rna-seq (expression analysis, inc, morrisville, nc), respectively. dna sequencing reads were aligned to human reference genome by bwa [17] and single nucleotide variants were identified using varscan version 2.3 [18] and were annotated using snpeff version 4.0 [19]. putative somatic mutations were prioritized by mutant allele frequency, recurrence and predicted functional impact. rna […]

VarScan institution(s)
Genome Institute at Washington University

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