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Description
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.
Categories
License
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.
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User Ratings
User Reviews
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Very useful. Thanks.
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excellent app
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Great tool. This guy is a genius!
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works great.
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We use VarScan at the Genome Center at Washington University to call variants in Roche/454 and Illumina/Solexa data.