VarScan 2.3.7

Variant detection in massively parallel sequencing data
VarScan - Usage screen for the application when running it from a terminal window.
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VarScan is a free and open source, platform-independent, technology-independent software tool for identifying SNPs and deals in massively parallel sequencing of individual and pooled samples.

Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequencyh.

Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples.

Main features:

  • Calls SNPs and Indels from SAMtools pileup files
  • Filters variants by coverage, read depth, variant frequency, and base quality
  • Determines somatic status (Somatic, Germline, LOH) for Tumor-Normal pairs
  • Compares, merges, and intersects two lists of variants
  • Limits variant calls to a set of target positions or target regions
  • Free for non-commercial use.

last updated on:
July 17th, 2014, 21:57 GMT
file size:
103 KB
license type:
developed by:
Daniel C Koboldt
operating system(s):
Mac OS X
binary format:
Universal Binary
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What's New in version 2.3.1
  • Expanded VCF compatibility for filter, somaticFilter, and processSomatic commands Extended the optional VCF fields for mpileup2snp, mpileup2indel, and mpileup2cns output to include all VarScan fields
  • Made it possible to provide a list of sample names for VCF output for mpileup2* commands.
  • Expanded copyCaller functionality to filter by depth and output candidate homozygous deletions
  • Fixed a bug in the indel-filtering functionality of the filter command
read full changelog

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