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.

Versions 1.20.0, 1.22.0, 1.24.0
License GPL-3
Links biotools: deepsnv


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