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Virmid

Estimate sample composition accurately or the level of contamination of a disease sample without genotyping. Virmid is a probabilistic method for Single Nucleotide Variation (SNV) calling. This application increases genotyping accuracy, especially somatic mutation profiling, by rigorously integrating the sample composition parameter into the SNV calling model. The robustness of this application makes it applicable for identifying mutations in other challenging cases.

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Virmid forum

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Virmid classification

Virmid specifications

Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Input data:
Some short reads sequenced from a pure control sample and a potentially mixed disease sample.
Programming languages:
Java
Version:
1.2.0
Maintained:
Yes

Virmid distribution

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Virmid support

Documentation

Maintainers

  • Vineet Baf <>
  • Sangwoo Kim <>

Credits

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Publications

Institution(s)

Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA; Department of Electrical and Computer Engineering, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, Rady Children’s Hospital, University of California at San Diego, La Jolla, CA, USA; School of Information and Communications, Gwangju Institute of Science and Technology, Gwangju, Korea; Department of Computer Science, Stony Brook University, NY, USA; Graduate School of Medical Science and Engineering, KAIST, Daejeon, Korea

Funding source(s)

Supported by the National Science Foundation (NSF-CCF- 1115206), National Institute of Child Health and Human Development (1P01HD070494-01) and National Institute of Health (5R01-HG004962, U54 HL108460).

Link to literature

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