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VarScan

Posted on by Robin Ding Leave a comment Bio-Informatics
5.0

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.

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Website http://varscan.sourceforge.net
Tags
License Non-Profit Open Software License 3.0 (Non-Profit OSL 3.0)
Platform Linux Mac Windows
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
  • Free for non-commercial use.