Variant Quality Investigation Helper

Imports Variant Calling Format file into R. It can detect whether a sample contains contaminant from the same species. In the first stage of the approach, a change-point detection method is used to identify copy number variations for filtering. Next, features are extracted from the data for a support vector machine model. For log-likelihood calculation, the deviation parameter is estimated by maximum likelihood method. Using a radial basis function kernel support vector machine, the contamination of a sample can be detected.


Reference manual

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1.0.0 by Tao Jiang, 15 days ago

Browse source code at

Authors: Tao Jiang [aut, cre]

Documentation:   PDF Manual  

GPL-2 license

Imports changepoint, e1071, ggplot2, stats, VGAM

See at CRAN