VarScan 2.3.5

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.

Here are some key features of "VarScan":

· 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.

Requirements:

· Java

What's New in This Release: [ read full changelog ]

· 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
· Fixed European locale parsing errors in the copyCaller command