This package provides provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs. The shearwater algorithm computes a Bayes classifier based on a beta-binomial 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.
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install bioconductor-deepsnv
and update with:
conda update bioconductor-deepsnv
A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-deepsnv.