VarScan 2.3.4
VarScan 2.3.4 Full Download Summary
File size: 82 kB
Platform: WinXP, Windows Vista, Windows Vista x64, Windows 7, Windows 7 x64, Linux, Mac OS X
License: Open Source
Price: FREE
Downloads: Total: 77 | This Month: 2
Released: 2013-02-04
Publisher: Dan Koboldt
Publisher URL: http://varscan.sourceforge.net/
VarScan 2.3.4 Full Description
The advent of massively parallel sequencing technologies has fundamentally changed the study of genetics. New platforms like the Illumina GAIIx and the Roche GS yield unprecedented levels of sequencing throughput. The analysis and interpretation of data from next-generation sequencing platforms presents a substantial informatics challenge.
VarScan is a platform-independent, technology-independent software tool 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 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.
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
Release notes:
New Release· A correction to the way that genotype quality (GQ) is calculated in VCF output. It had been 0 - log10(p_value), but the correct calculation is 0 - 10 * log10(p_value)
· Changes to VCF output, particularly for indels, to meet VCF specification standards
· A new option to provide a file of sample names when calling multiple samples using mpileup files (--vcf-sample-list)
[ VarScan full changelog ]
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