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Virmid

Virmid

A tool to detect impurity and somatic variation, single nucleotide polymorphism (SNP), in somatic tumor sequencing data. The Virmid algorithm uses maximum likelihood estimator (MLE) for the joint probabilities of control and disease genotypes and sample contamination level.

Topic

Genetics; DNA polymorphism

Details

  • Operation: SNP detection
  • Software interface: Command-line user interface
  • Language: Java
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Not stated
  • Cost: Free
  • Version name: 1.2.0
  • Maturity: Stable
  • Credit: The National Science Foundation, National Institute of Child Health and Human Development, The National Institutes of Health (NIH)
  • Contact: Sangwoo Kim sak042 _at_ cs.ucsd.edu | Vineet Bafna vbafna _at_ cs.ucsd.edu
  • Collection: -

Publications

Kim S, Jeong K, Bhutani K, Lee J, Patel A, Scott E, Nam H, Lee H, Gleeson JG, Bafna V "Virmid: accurate detection of somatic mutations with sample impurity inference." Genome Biol. 2013 Aug 29;14(8):R90. https://doi.org/10.1186/gb-2013-14-8-r90
PMID: 23987214
PMCID: PMC4054681


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