varscan to run in linux online online with Winfy
We have hosted the application varscan to run in linux online in order to run this application in our online workstations with Wine or directly.
Quick description about varscan to run in linux online:
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 GITHUBFeatures:
- 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.
Audience: Science/Research.
User interface: Command-line.
Programming Language: Java.
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