VarScan 2.3.7

Variant detection in massively parallel sequencing data

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What's new in VarScan 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
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LICENSE TYPE:
Freeware 
FILE SIZE:
103 KB
USER RATING:
UNRATED
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DEVELOPED BY:
Daniel C Koboldt
CATEGORY:
Home \ Math/Scientific
1 VarScan Screenshot:
VarScan - Usage screen for the application when running it from a terminal window.
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.

Last updated on July 17th, 2014

Runs on: Mac OS X (Universal Binary)

feature list requirements

#identify snp #sample seqeuencer #snp identifier #identify #snp #sequence #identifier

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