This is the Linux app named VarScan whose latest release can be downloaded as VarScan.v2.3.9.jar. It can be run online in the free hosting provider OnWorks for workstations.
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Variant detection in massively parallel sequencing. For one sample, calls SNPs, indels, and consensus genotypes. For tumor-normal pairs, further classifies each variant as Germline, Somatic, or LOH, and also detects somatic copy number changes. THE LATEST VERSION IS AVAILABLE ON GITHUB
- 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.
This is an application that can also be fetched from https://sourceforge.net/projects/varscan/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.