VarScan specifications


Unique identifier OMICS_00094
Name VarScan
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


  • mpileup2cns
  • somatic
  • copynumber



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VarScan articles

VarScan citations

PMCID: 5891033

[…] 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 […]

PMCID: 5732697

[…] (30–2149x). for each sample alignment and variant calling was performed within miseq reporter (illumina) tool available in the instrument. additionally, an independent variant calling was done with varscan 2.4.0 [43] and annotation with annovar [44]. all the variants identified by both complementary methods were visualized using igv and only those mutations detected in both pool a and pool b […]

PMCID: 5706097

[…] sam tools. in order to identify somatic snp and indel mutations, the obtained bam files from both blood cell and plasma samples for each patient were processed for pairwise variant calling using varscan (v2.4.2) 21 using the following parameters: i) minimum coverage for calling somatic variants in blood cell samples is 8, and 6 for calling in plasma samples. p-value threshold to call […]

PMCID: 5070570

[…] picard v1.46. reads with a mapping quality of zero, or that were marked as duplicates by picard, were excluded from further analysis., putative snps and indels were called in the exome data using varscan 2 and the following thresholds: coverage ≥8x, phred base quality ≥15, minimum variant allele frequency ≥10%, and fisher exact test p value <0.05 [23]. false positives were removed […]

PMCID: 4704711

[…] two strains used to make the parental strain. integrative genomics viewer (igv) was used to visualize and browse genomes (robinson et al. 2011). single nucleotide variants (snvs) were called using varscan with the following parameters: –min-coverage 3 –min-avg-qual 5 –p-value 0.1 –str-filter 0 –min-freq-homozy 0.9 (koboldt et al. 2009). to identify strain-specific events, each sequenced strain […]

VarScan institution(s)
Genome Institute at Washington University

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