This package provides provides quantitative variant callers for detecting subclonal mutations in ultradeep (>=100x coverage) sequencing experiments. The deepSNV algorithm is used for a comparative setup with a control experiment of the same loci and uses a betabinomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs. The shearwater algorithm computes a Bayes classifier based on a betabinomial model for variant calling with multiple samples for precisely estimating model parameters  such as local error rates and dispersion  and prior knowledge, e.g. from variation data bases such as COSMIC.
Package details 


Author  Niko Beerenwinkel [ths], David Jones [ctb], Inigo Martincorena [ctb], Moritz Gerstung [aut, cre] 
Bioconductor views  DataImport GeneticVariability Genetics SNP Sequencing 
Maintainer  Moritz Gerstung <[email protected]> 
License  GPL3 
Version  1.24.0 
URL  http://github.com/gerstunglab/deepSNV 
Package repository  View on Bioconductor 
Installation 
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