VarScan is a Java-based tool that is specially designed to be a platform and technology-independent utility for identifying SNPs and indels 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 frequency.
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
Requirements:
· Java
What's New in This Release: [ read full changelog ]
· Corrected VCF output format for mpileup2snp/mpileup2indel/mpileup2cns, particularly for indels
· Corrected a bug that was causing non-variant or different-variant lines to be output in mpileup2snp/mpileup2indel
· Addressed a bug that incorrectly counted reads at positions where no consensus call was made (CNS="N"),
· which sometimes producing reference-supporting read counts (reads1) of less than 0.
· Corrected a bug that was causing incorrect GC content calculations in the copynumber command
· Removed the warning about invalid mpileup for sites with read depth=0.
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